The new owner has since failed to pay utility bills in one of the two building, causing it be condemned.

What your considering here is some franken-sale "monster" of twisting these 2 into a manner neither was ever meant to be utilized as. 

In my market, STR with pm, utilities, and furnishing costs is about on par with LTR without PM.  

In my experience, only about 75% of these huge closing credits can actually be utilized and the majority of that goes to egregious "upgrade" fees to the builder anyhow. 

In the Seattle market, condoizing costs around 15K (survey, site plan, recording fees, legal fees, HOA creation and coaching from lawyer, setting up utility sub-metering if required).

-Those utilities will be connected to the main residence unless you get new separate meters permitted and added.

I plan on reaching out to a few owners in the area and seeing what their commercial lease agreements are like but I was wondering how other investors determine to ask for certain payments towards (taxes, utilities, Insurance, etc.)

House hacking will build skills and equity while staying at home would (ideally) save more money (utilities, food, consumables).

Sell a property with an existing low interest mortgage utilizing a mortgage wrap.

A different/maybe possible way to go about it, is to find a plot with utilities on the outskirts of your town (may not be possible, I have no bearing on your local market), then buy a mini home.