Should I take Deutsche Bahn/OBB or just fly from Vienna to Berlin

What about "the DB experience" are you concerned about? The night train to Berlin is a Nightjet, ÖBB's night train brand. Even if it's probably hauled by DB in Germany.

I'm worried it arriving late in Berlin and then I have the chance to miss my flight home.

When is your flight?

Flight is at 2 pm on a Tuesday, and the train arrives in Berlin Hbf at 6:30 am the same day

So it is an IC train that runs through Germany. Operated by OEBB, but will have a German crew.

Is your flight a direct flight to North America, or a connection at another European airport?

It's a flight to North America, it has a stop over but is considered international, so longer security.

You have about a 3 1/2 cushion, but I just wonder about a 12 hour overnight train sitting in a seat, then getting on an Intercontinental flight with one intermediate stop. Sounds exhausting to me, but then I am old and spoiled. I'd fly the night before and get a good nights rest.

So if the train arrives 6:30 and your flight leaves at 14, that is 7,5 hours margin. I would not be worried about that.

but I just wonder about a 12 hour overnight train sitting in a seat

You don't have to spend the trip in a seat, you can book a bed if you want to sleep.

The fastest trains just take about 4 hours from Munich to Berlin. But you really should go the night before in case there are any issues that come up.

I'm still amazed that there are trains going so often day and night on that one route.

You don't have to spend the trip in a seat, you can book a bed if you want to sleep.

I do not believe IC 296, departing Vienna at 19:13 and arrives the following day at Berlin Hbf at 6;30, has any beds. It snakes its way through Austria and Germany during the night, making 23 stops along the way. ,
If you want a bed, you need to book NJ 456, departing Vienna at 22:10 and arrives the following day at Berlin Hbf at 8;15,

I definitely don’t mind the seat and like train travel a lot, my main concern being the timing and how long a delay on DB trains usually is if any.

This is a toughie. I would not be too concerned about missing the flight in Berlin. One one hand, it IS peace of mind to be in the city you fly from, but on the other, a nightjet may save you money on a hotel room that night. Then you're in Berlin, store your luggage at the station, enjoy your morning, then head to the airport.

I prefer the train. Just getting to the airport, security, flying, out of the airport, train to Berlin, check in, train back to the airport...phew. Only way I will do that is if I just get a hotel by the airport so that I can just walk to the terminal.

I do not believe IC 296, departing Vienna at 19:13 and arrives the
following day at Berlin Hbf at 6;30, has any beds. It snakes its way
through Austria and Germany during the night, making 23 stops along
the way.

You're right! It's one of their new IC-trains and it only has seats. https://www.bahn.de/service/ueber-uns/zugtypen/ic-2#Bildergalerie-IC2-KISS

For some reason, my brain thought is was the Nightjet the OP was considering.

It's a flight to North America, it has a stop over but is considered international, so longer security.

Where is the stopover?

The issue would be whether you need to do Schengen-exit passport processing in Berlin that would add time to the process, not security

Flights are so cheap between Vienna and Berlin. I’d definitely fly the night before.

Unfortunately a flight is about 140 € so not super cheap, compared to the train.

I always take the OBB night train for this Berlin-Vienna route. One other difference I noticed doing the night train option between OBB Night Jet and the IC operated by DB. I took the IC last summer from Stuttgart to Wien Hbf....crowded enough, at least my coach in the general seating area. The lights never go off in the IC as they do on the OBB Night Jet if that is a concern....no problem , I still slept.