Bayern Ticket - Seefeld and Zurich

a) For Munich to Seefeld, you can buy a Regio-Ticket Werdenfels + Innsbruck for 58.50 EUR for 3. That would save you about 14 EUR vs the Bayern Ticket plus 3 point-to-point tickets to Seefeld.

b) Zurich to Munich, the Swiss Travel Pass will cover you to St Margarethen, Then a Bayern ticket for Lindau-Reutin to Munich for 45 EUR as long as you use the Regional train from Lindau-Reutin. so then you just need to pay for the short stretch through Austria from St Margarethen to Lindua-Reutin.

Thanks Sam, that is really helpful. I hadn't considered the Lindau route on the way back to Munich, but that makes perfect sense to cover with the Bayern pass. Appreciate it!

For Zurich - Munich you could indeed use a combination of a ticket st. Margarethen - Lindau and a Bayern ticket. However that will require you to take only regional trains in Germany. That means a longer trip, and several transfers.

If you want to take the EC train do the following: Buy a ticket st. Margarethen - Munich on www.bahn.de. If you buy this in advance you can get a Sparpreis Europa, which is usually a good deal. With your pass, and that ticket you can then just take the direct EC from Zurich to Munich.
(Note that from Austria to Switzerland the border station is Buchs, so you need a ticket till Buchs, and from there on you use your pass).

Zurich to Munich, the Swiss Travel Pass will cover you to St Margarethen, Then a Bayern ticket for Lindau-Reutin to Munich for 45 EUR as long as you use the Regional train from Lindau-Reutin. so then you just need to pay for the short stretch through Austria from St Margarethen to Lindua-Reutin.

I'm not sure if this ticket splitting strategy is worth it here. A Europa Sparpreis ticket from Zurich to Munich from DB costs approx. 39€ pp = 117€/3 (same price from St. Margreten). Combining tickets for transit through Austria (3 x 9.30) with the Bayernticket amounts to about €73.
But for the savings of €44, you get at least one additional change (in Lindau-Reutin) and an hour longer travel time (arrival 14:05 instead of 13:04; in theory, you could choose a connection that arrives in Munich as early as 13:39, but that has an additional 3-minute transfer in Buchloe, and I wouldn't bet on that working out).
Maybe the swiss pass can be shortened by one day and thus the price difference can be recovered?

Thanks for the extra options WengenK and sla019. I wasn't aware of the option for Europa Sparpreis, and that really does seem to be the best option. I don't mind paying a little more for time savings - that is a long train day anyway. Our travel pass is a swiss half fare, so it will be useful that day whether we use it for the zurich north part of the trip or not.

Note that the Super Sparpreis Europa Ticket is nonrefundable, like an airline ticket and prices go up as you approach your travel date. The best price will be today, so if your itinerary is set enough that you know exactly when you will depart Zurich, it is safe to buy. If you want to maintain flexibility, use the Bayern Ticket strategy.

Looking 4 weeks from today, the Super Sparpreis Europa tickets is 39.90 EUR per person. There is also a Sparpreis Europa ticket for 45.90 EUR per person is cancelable up to the day before departure for a fee and a voucher for future travel. The walk-up price is 91.20 EUR per person.

Thanks Sam! I was eyeballing the Sparpreis for the flexibility. I didn't realize the price differentiation on walk up. I will get the plans nailed down and purchase the tickets!