If it’s three separate units all separately metered and permitted through the city, they should use other multi family properties as comps, right?

Different designs cost different amounts to pull off.What are the building and permitting requirements of the area the garage is in?

If the repair need is more extensive than that, you'll need him to sign off on the repairs anyway for your building permit.

In March of 2014 a pipe burst and she got permits and an estimate for repairs of $23,000.

The costs included in the $1 million cost figure would be land, construction materials, construction labor, professional fees, permits and so on.INVESTOPEDIA EXPLAINS 'LOAN-TO-COST RATIO - LTC'The LTC ratio helps commercial real estate lenders assess the risk of making a construction loan.

This was also permitted for and passed county inspection.  

If this was a potential deal I was reviewing and based on the information you provided, this is how I would approach it:1) I would ask that Structural Engineer who performed the inspection of the foundation to issue you, at the Seller's cost, a current HUD Foundation Certification or Foundation Approval Letter which should include a) Distress Analysis and b) Manometer Survey effective January 2015. 2) Since the Owner agreed to bring the Electrical "Up to Code", I would be looking for an Opened/Closed Permit -OR- a completed 3rd Party Electrical Inspection Report to verify the work was completed "To Code".3) If a Pipe Bursted, one has to ask is the Heating System working and are the walls insulated properly and if so then why did the pipe burst.

Appraiser's are not permitted to advocate. 

As a newcomer to real estate I think the advice you gave is something to remember Great jobKeep learning, keep earning. 

You can look up the address of the house on the building inspection web page, and look at the history of what permitted work has been done (or not done.)