Their reason for declining was "The subject property is a legal non-conforming use that cannot be rebuilt to it's current configuration and density." 

Also the row configuration.

Oh, and we actually don't have any common space registers in our building.From the quotes I'm getting that separate systems configuration is going to cost us almost $30k all in, which is over twice the price of replacing the boiler and 4 individual hot water tanks with a single system. 

We have re-configured the floor plan, fully updated all of the finish-outs, fixed the foundation, roof, fixed the concrete, and put in a new AC unit and moved it to the attic to have more efficient use of the square footage of the house.

Also, the repairs & maintenance, insurance and CAPX exceeds typical % rules of thumb because 10% of a small number isn't enough to pay for a roof, HVAC, etc. and those costs are not cheaper in a cheaper house.I assume you are planning to self manage, but I would call several PM's and ask them their opinion on market rents at that address and for your configuration.

What is nightly home rate for configurations having same number of beds/baths as yours?

Business entities, most of the time people use LLCs in various configurations.

Brand new 27inches wide with an electric glass cooktop & an oven, same configuration.

I do plan to switch to a pitched roof when the time comes where patching and painting out weighs the new roof configuration.

We're working through what the most advantageous configuration is.