@Matthew SlaughterDid the lead inspection you had performed say that no lead was present or that lead is present and was in conformance?

You need to get commercial financing since legal entities are not eligble for conforming residential loans.

Also, you are living in the property which should negate the limited liability of the legal entity (consult a qualified professional or two).Legal entities such as a LLC are not eligible for conforming residential loans. 

@Alex JonesThe issue with legal entities, such as LLC's, is that they are NOT eligible for conforming residential loans. 

If it’s a part of the main structure and conforms with the rest of the home in terms of building components, heated and cooled sufficiently, etc. it should be included in the GLA of the main structure and should not be valued any differently.

I know it will be just as much a re-sale consideration in a decade as it is for me currently, but since I see this as a long-term buy-and-hold, the more immediate concern is determining ARV and what it would appraise for when the time comes to back into a conforming mortgage after seasoning (BRRRR style). 

However, you do "pay" for the LLC in terms of needing commercial loans since legal entities are not eligible for conforming residential loans (I post on that a great deal about those people who move their Title back and forth --- bad idea in my opinion). 

From an appraisal standpoint, you may want to look into whether or not it will count as added square footage and that the bedrooms will be conforming.

I"m seeking to rezone the lots as they are pre-existing, prior to the first zoning codes, which later came in and only granted duplex zoning, so these are legal, non-conforming but can't be converted to separate up/down "condo" sales as lenders won't loan if a structure can't be rebuilt after a catastrophic loss unless its zoned correctly as their collateral is compromised and that is the case in the county where these are located. 

If you buy a property in your own name, you might go after a conventional conforming Fannie/Freddie type loan.