I have 2 story house with the basement. 3/1 with opportunity to add second bathroom on the second floor.  

We wanted to do LVP throughout the house and the kitchen and bathrooms had an extra layer of plywood to raise its height so we had to manually crowbar it out, which took days and a lot of work.Aside from the flip, we didn't expect the sellers too keep changing their minds on closing date.

Asset over $1k/ft is likely to value from an added bathroom significantly more than an asset valued at $500/ft.  

He permitted me to a recreational building permit so I can finish it but limits it from a perm bathroom and kitchen and he came as close as possible to saying after inspection I’m fine to do whatever.

The in-place plumbing will overkill, so if over time you lock and shut down a couple bathrooms (so you have less to maintain), whatever. 

It sounds like the bathroom would be added to your primary residence so it partially depends on when you would look to sell the home or start otherwise renting it out.

Try looking into zillow/Redfin and see what your potential rents you can get near the neighborhood by filtering the bedrooms/bathrooms of the intentional property that you are planning to buy.

Then I calculate that replacing the roof, HVAC, and remodeling bathrooms/kitchens would cost $400,000.  

In order to minimize the potential for mold growth in the property, Resident(s) must: *Keep Premises clean, especially the kitchen, bathroom(s), carpets and floors.

I think a strategy that would serve me well is one where I buy a 2 (or 3) bedroom house with 1.5+ bathrooms.