We'll be doing a lot of train travel this fall in the above countries. I'm pretty sure I have the best passes, point-to-point fares, etc. figured out for this trip. When I buy tickets in one country for a route that ends up in another, will the first country figure in the pass or discount for the other country? For example, Zurich to Regensburg Germany. We'll likely have Swiss Flexipass Saver and a German Pass .
With rail passes you shouldn't have to "buy" tickets. As long as the passes are validated for that day, the Swiss pass should cover you to the Swiss border, where the German pass will become effective. Just show the validated pass to the conductor. Note: if you go around the east end of Bodensee, you'll go through a little bit of Austria, and you will need a valid Austrian ticket for that section. Note: without rail passes, you could buy online, advance purchase discount tickets from Zurich to Regensburg (change in Munich) for €39 per person.
For group travel within Belgium, do not bother with any 3rd party passes. Belgian rail sells their own pass that allows for 10 trips anywhere within the country for about 60 euro. The huge advantage here is that more than one person can use the pass simultaneously. For example, a round trip from Brussels to Brugge for two people would count for 4 of the 10 trips.