One more design earthquake later - more of a tremor, actually - and the design is now at 2000 gross square feet. This is the total area of all 3 floors, calculated from the exterior surface of the exterior walls. At 28' wide, the house can easily fit on a 40' wide urban lot. As such, I feel that I've finally been able to achieve the size goal I was after. And it seems to flow better. And have a more natural internal flow to the roof deck.
BUT: Is it too small? Testing furniture layouts in all rooms, it seems like everything works pretty well, but the house has gone from 3 bedrooms + a multi-purpose guest room / office + studio to 2 bedrooms + a multi-purpose guest room / office + studio. A realtor could see it as a 4-bedroom house, but I see it as a 2 bedroom with some flexible rooms that in reality would end up fixed in function. Is this too much of a compromise? Also, I have advised many clients and friends over the decades that anyone who doesn't build out a full basement when they have the chance will come to regret it later. This current house design does not have a full basement! If it did, the house would be 564 square feet larger: a crime! Right? Plus, more space means more space for stuff, and therefore less impetus to purge stuff that you really don't need anymore or can live without, and that's un-American. Right?
The logical next step is to define the house with and without the basement fill-out and find out how much the additional cost would be. Since it could be seen as unfinished (but heated) space and would not include a bathroom, it would be "cheap space". (I tell that to clients and friends, too.) But even "cheap" costs something, and I have a cheapskate mentality at the moment. Wait and see.