Just to be clear, 16949 is "the Mrs" and she's the one that is buying the house.
I dont think she's looking to alter the actual layout of the house. It sounds like she found an house that is an automotive lover's dream already. Did you look at the floor plan that she posted?
Also, I dont necessarily agree with the whole "dont change it in case you sell it" mindset. Your house is your home. Unless you really see this as a stepping stone, I say make it the best house for you to live in, exactly as you want it. If you end up selling it down the line, you can make adjustments then. Dont let the fear of someday selling prevent you from having what you want. Its the same way with any DeLorean; unless you're buying it to resell it, dont not build the car you want just because someone else might not like it.