Lender A misses this or doesn't have this knowledge and then tells you a week before closing that your rate is changing because the program they quoted wont work once the issue is caught. 

They are paying for some repairs now after I've had several issues and a brand new tenant moved out, but I'm still paying a mortgage without any rent coming in during those months. 

The reason sellers cannot sell these properties through the traditional market is often due to certain issues, and 98% of the time, these issues are not beneficial to you as a buyer.

The interior was outdated, the landscaping was overgrown, and several deferred maintenance issues were apparent.

You are micro-analyzing the minutia of each offering, but that's not really the issue.

The economy is not as stable as it appears, this is the type of event that can cause a tangible issue.

Purchasing a STR in a somewhat sketch area is a terrible idea and as others have mentioned, is going to open you up to potential issues. 

The foundation was already approved, permitted and finaled years ago for a 3400 sf house, and its solid and I won't be building directly on the overhang edge; but rather back away from the edge a few feet to prevent any load issues all the weight will be on the longer sides of the existing footing.

I've been teetering around the idea of house hacking once I am done with college, but a big issue I have come across when speaking to a mortgage broker is the fact that I need to prove 2x of the mortgage in monthly income.

Usually an issue if older door is salvaged and new locks are installed that don't quite match up with the old door strike plate location.