Generally speaking, you will not have access to the interior to determine its condition prior to the application, nor at anytime during the process.These are not programs for the faint at heart, and none of them will permit wholesaling or assignments of contract, so if you pursue any of these, be prepared to put the money in once it's yours.

I'm finally in a situation in which I've been able to work with a small bank to do portfolio loans bit was recommended to create a LLC prior to doing.

How accurate is comparing properties by their price per sq foot?

The appraiser comes in and ignores the fact that my home is zoned R-20 and stated highest best use the home is commercial and my comparables are not conducive to the property, which I believe this is ludicrous. 

Value your property based on comparable recent sales NOT Zillow estimate. 

I'm thinking about this from the perspective of comparing to renting, which just seems to keep getting more and more expensive—at least if I own a place I can lock in a rate, build equity over time, and potentially (though not certainly) look forward to some appreciation.

The problem I am having is getting comparable properties within the area.

About 1350 addresses that had the following criteria 45+ years old, 40 to 100 percent equity, SFR, owner and absentee occupied, and was purchased no earlier then 3 years prior.

This is used to compare 1 property against another. 

I have 12+ years in construction and management which makes building new homes much easier for me, as I can plan everything prior to construction and work out any major issues before construction begins.