It was not uncommon that they bought some of the worst houses (weird layout, dated, much deferred maintenance) in the nicest neighborhoods and then would try to relist them as-is to make a profit before ending up having to do the actual work required to the property for it to sell again, selling at a loss, or maybe making a little bit of money in transaction fees.

For example, the layout of one kitchen might lend itself to adding a dishwasher easily.

Why give burglers a layout of your house and your belongings?

I don't have a magic wand to help you move forward but I would just lay out your possible options: 1. 

Next I intend to cross check the calculations (esp. taxes) and simplify the layout.

Big layout and frankly it feels like a cult.

. - if you need two stairwells and an elevator, that will of course drive costs way up and it also eats into your floor plate area and can crush layouts on a smaller building, possibly turning your small CMX2.5 lot you'd planned to build 5 stories on into what may as well be a CMX2 lot and allow only 3 stories, since you can't actually fit 2 stairwells, an elevator, a hallway all the way through from front to rear, a small lobby, a mail room, etc.

Their approach to sub-portfolios is intuitive and flexible, and it was easy for me to tweak a "portfolio" to have it track my income and expenses from my real estate agent gig.

An existing kitchen layout might work well for adding a dishwsher or microwave hood for example allowing it to be made functionally modern without a major rehab.

Intuitively, probably just do a price reduction because once you open up walls, who knows what else you might find.