Unless the comparison includes permit checks, zoning check, walk through of the property prior to the sale (to see interior of unit), disclosures, plumbing and foundation inspections there is no way to compare values and having purchased mostly off market properties I can state with fact that the value is not easily discernible. determining a property has a failed sil plate or needs 100’ of new sewer run is not easily identified.  

Don't do it withour a permit.

When looking into it briefly, it looks like Mackinaw City, Traverse City, & Petoskey are the most restrictive on AirBNBs whereas Boyne City and Harbor Springs allow them with a permit, any information on how difficult it is to get one of these permits for an out of state investor?

There would be many more hoops to jump through with zoning and permitting.

You can also expect complaints of noise, trespassing, etc.If the situation permits, I recommend only allowing it for a significantly higher price and additional requirements in place.

If you average permit filed price per square foot its about $135-$140 traditionally for the builders because they are adding basements.

Have the permit in hand, the building erected quote, banker says no downpayment needed since it is tied to an existing project that is very LTV favorable.   

Quote from @Marty Rogachefsky: I permit a few small nail holes per wall, or they can use command strips.

However, this time around, things have not been going as well.Six months ago, I entrusted my property manager with hiring contractors and obtaining the necessary permits to get my property rented.

YOUR PERMITS.