In my case, a home I am looking for is above market rate, and their justification is that is should be valued like a commercial property with past revenue and net accounted for. 

Depending on your specific situation, it is possible that we could find a justification for treating it as a repair. 

Despite the fact that some markets were faced with 200% YOY increases this/last year, there doesn't seem to be a justification for this UW assumption.

They sent a very professional slide pitch deck that showed all of their justifications around that specific market, e.g. employment market, housing shortage data, the new developments in the area, the air bnb data, etc. etc.They also stated the numbers were conservative (7 year to reach the target returns) and that likely it will be year 4-5.

Criticizing others for their failure to do the same provides them self-justification for their confirmation bias.This is a common behavior pattern to justify many debatable decisions people make in life.

The tenant threatens to get lawyers, my concern is their safety, but I can’t get any justification to make improvements to the property for security.

I've heard of other PM's keeping late fees and using the justification that it's payment for their efforts in notifying late tenants and chasing that late rent.

Hey Hyeonji, are you referring to a DPA program specific to Santa Clara or just if DPA in general is possible in Santa Clara?  

. $15k Fee Justification: I’m trying to understand what the $15k fee actually covers, especially since it appears that Martel and the assigned team also take a cut from every deal (contractors, project managers, lender kickbacks, etc.).

That's because most appraisers aren't actually looking to determine a real value for the property, but rather just looking for justification of the already agreed upon purchase price.