"if I miss my train" question

If you miss the train because of a flight delay and have to leave on a later one, you will have to purchase another ticket or risk a €60 fine. The easiest thing to do would be to install the DB app on your phone, establish an account, and then grab the train and buy the ticket online once you board. If you have time, you can buy it at the station but I wouldn't risk it.

Same procedure for earlier train.

I am assuming that your ticket is one of the Super Saver fares that is locked into a specific day/time. If not, then you don't need to worry about it. If you haven't bought your ticket yet, you may want to check and see if there is a ticket you can buy that will allow you to catch any train that day. It will be more expensive than the Super Saver but less expensive than a fine or buying 2 tickets.

Planes and trains are not tied together. If the plane causes you to miss the train, then it is your problem and expense. If you hold a connecting train ticket and miss a train because the first train was later, then a trip to the ticket window will get you a new ticket on the next train. Never get on a train without a ticket for that specific train. In your example I would not buy a ticket till I was on the ground.

Thanks so much for the quick, excellent reply.
Have not purchased tickets yet and will now probably buy a non-saver fare for the flexibility and the possibility of both earlier & later trains.
So can I assume that with a non-saver fare I can just board the next train and deal with it then (with app or train staff)?

Here are the Terms and Conditions for the “ Flexpreis Europa”fare for the direct ( no changes) EC train from Munich to Bolzano:

Flexpreis Europa (Outward journey)

Conditions
With an ICE ticket you can use all trains on the day of travel, with an IC/EC ticket you can use any Intercity or >Eurocity as well as local and regional trains.

If you choose a train service that is subject to reservation, your booking already includes a free seat reservation >for this train service. If you choose a different train at a later date, please book a new seat reservation possibly >subject to a charge.

In many cities your ticket is also valid for local public transport, both on the outward and return journeys. >Departure and destination points must be within the tariff zone permitted by the City-Ticket. You can find the list >of permitted cities by searching for "City-Ticket" on www.bahn.de.

Exchange / refund
Cancellation (exchange or refund) before the 1st day of validity free, thereafter 19,00 EUR.
Conditions

Since the direct EC train only runs every 2 hours, it is unlikely you would make an earlier train. And if you just miss the train you booked, you may not want to wait the nearly 2 hours til the next EC train. It it sounds like you are free to choose the intermediate journeys on regional trains, with 3 changes on the way, if you want.

if we miss the scheduled train due to flight delay or whatever, there are multiple later trains, but what is the procedure for continuing on a later train?

That depends on the type of your ticket. If you have a (Super)Sparpreis you are out of luck. If you have a flex ticket, you just hop on the next train or whichever is convenient for you.

get on board & deal with it there

Please don't do that. Boarding the train without a valid (!) ticket will result in a hefty fine.

There could be a couple of "work-arounds" here, but it depends on some thing you haven't told us.

What is your scheduled time of arrival in Munich. and what was the departure time of the EC (from the Hbf or Ostbhf) that you intended to be on?

What was the price you saw for the Super-Saver-Ticket you wanted to buy (or the SaverFare-Ticket)?

On what airline are you flying to Munich?

Do you have to get to Bolzano the same day you arrive in Munich, or would you be willing to stay in Munich for a day, see a few of that town's sights, then travel to Bolzano the next day?

More details as requested:
What is your scheduled time of arrival in Munich.
0745
and what was the departure time of the EC (from the Hbf or Ostbhf) that you intended to be on?
S8 @ 0904-0935
EC83 @ 0944
I realize that catching the S8 @ 0904 is an optimistic scenario which is why I'm validating my backup
plan of catching the next EC83 @ 1144 if necessary. I've been thru MUC a few times before and I know plan #1
is possible if my flight isn't late and there are no other slow down issues.

What was the price you saw for the Super-Saver-Ticket you wanted to buy (or the SaverFare-Ticket)?
Actually I have not looked at prices closely... more concerned about timing. But the (DB website) Left fare was about 70 euros
and the Right (probably flex) fare was 140 euros... note that I have no problem paying extra for flexibility & reduced stress

On what airline are you flying to Munich?
Air Canada

Do you have to get to Bolzano the same day you arrive in Munich, or would you be willing to stay in Munich for a day, see a few of that town's sights, then travel to Bolzano the next day?
Yes I do need to get to Bolzano same day as arrival. I have a spare/safety day built in but don't want to spend it travelling
but de-jet-lagifying in Bolzano.

Thanks to all for the feedback I've received.

OK, so staying a day in Munich and then taking the EC with a SuperSparPreis ticket, when you know you can catch the specified train is out (since you want to get to Bolzano that day).

A suggestion I would have made if you were flying Luftahansa, United, or American was to use a Rail&Fly ticket. Rail&Fly is a program the Bahn has with some partner airlines, the ones I mentioned above, but not Air Canada, where they issue you a "flight coupon" good for any train in the Bahn system, including long distance trains like ICEs, ICs, or ECs, to get from your arrival airport to any station in Germany. The ticket is valid the scheduled day of arrival and the next day. The price, the last time I found it, was about 33€/P each way. So for 33€ each, you could have gone on any EC to Kufstein, Austria, a border station for the Bahn. From there the price of an open ticket for EC to Bolzano is 46€. Total 79€, and you don't have to get off in Kufstein, just change tickets.

Since Air Canada does not accept Rail&Fly, my next suggestion would take a little longer, but cost less. Take the same S-Bahn to Ost Bahnhof and catch the next BRB to Kufstein using a Bayern-Ticket for 26€ for 1 person, 34€ for 2. Get off in Kufstein and catch the next EC (with an open ticket pre-purchased for 46€/P). So the cost of tickets is 46€ plus half of 34€, or 63€.)

The trip from the airport to Kufstein using the BRB take 24 minutes longer than by EC including the difference in transfer time at Ost. (Actually, the transfer time to catch the BRB is 18 minutes; it's only 9 minutes with the EC. But the ECs run every 2 hours, the BRB every hour, and the S-Bahn on a 20 minutes schedule, so transfer times depend on a lot to things.) And then there is the transfer time in Kufstein. So it will take longer this way, but there is no risk for your ticket (unless you plane doesn't arrive that day).

BTW, for the record, the EC leaving Ostbahnhof at 9:44 is EC 83. The one at 11:44 is EC 85; the one at 13:44 is EC 87, etc.

Having flown into Munich a number of times, I can see where, if your flight arrives on time (7:45), you should be able to clear immigration and get to the S-Bahn station in time for the 9:04 S-Bahn to Ost, particularly if you are doing carry-on only. However, in my last 11 flights to Germany in this century, I have been an hour late arriving 2, maybe 3 times, so making the 9:04 is not a given.

If you buy to full fare EC tickets from Ostbahnhof to Bolzano and pay full price (153€, I think) and you make the 9:04 S-Bahn, you will get to Bolzano at 13:27. If you miss that S-Bahn and use the next EC all the way, you don't have to leave the airport until 11:04, and you will get to Bolzano by 15:27. To get to Bolzano by 15:27 using the Bayern-Ticket, you'll have to leave the airport by 10:04.

So, what would I do? The flexible fare for two people on the EC from München Ost to Bolzano, including the S-Bahn to Ost is 2 x 76,70€ or 153,40€. The lower fare using a Bayern-Ticket and flexible fares from Kufstein to Bolzano is a little more than 25€ less, 128,-€. I think I'd take the 25€ more and get the fully flexible fare ticket. That's the only way you could get to Bolzano by 13:27. I think you could do that fairly certainly if the plane was on time. And I think I would purchase the full fare ticket online in advance so that I would have a better chance of making the connection if times were tight.