They're just going to fix stuff, that either didn't meet local code, or missed their "standard" building practice. 

Depending on the lender and the product if it is non-comforming you may not need to wait that time and you may not receive a LE or CD, but still most lenders will have it as a standard practice to be safe.

and, have good, to very good, vetted property teams in different metros, and detailed quality standards.

Say for example the standard commission for a new tenant is 6% with half going to your agent and half the tenants agent then that would be 3% going to the tenant agent.

When I confronted them, they defended their quote, stating that they go off the industry standard and a portion of the labor time is for "testing the system after repairs to ensure safety."

Getting a new roof is important for ensuring that the property meets the standards required by most loan programs.

A deposit is standard for DD and maybe to pay for the appraisal.  

Quote from @Jose Almonte: The standard around the country is for the tenant to pay utilities. 

Bizarre times.Overall, this screams bad internal process, but it could just be a complicated deal. 

In many places, a "standard" residential district zoning (e.g.