This may sound like a dumb question, but if you are having a house custom built, why limit yourself to using the garage for your trains?
If none of the bedrooms are big enough, why not build a house with a bonus room, like maybe a finished room over garage (FROG). If you are not into formal dining (my wife and I aren't) you could also convert a dining room into other uses, like trains or crafts.
I have a couple of great storage cabinets and have moved to a carpet layout in our rental home (sold our last home of 25 years, six months ago). So, I'm thinking I may not even have a permanent layout in my next house (2 - 3 years).
Jim