Their numbers may be correct but they're not very good.

As long as the investor was good with the price you gave them, they won’t care that you are making money and most are actually happy that you are.  

There is a good chance they would limit the loan amount based on either appraisal, or purchase price + improvements (ie project cost), whichever is lower.

For example, if a 1,600 sq ft main house is appraised at $100 sq/ft, what could I expect a 600 sq ft ADU of similar build quality to be appraised for?  

Welcome to BP and good luck with the new ventures. 

@Kelly Flippinhappy to help but not enough in your info in your post to know if the house is a good deal or not. 

Yes, to qualify as a real estate professional, either spouse must meet the 750-hour requirement of material participation, where more than half of their personal time/services must be devoted to real estate activities.If your spouse works another part-time or full-time job, it may be difficult to demonstrate that more than half of her working hours are focused on the real estate business.If not, you should qualify as you exceed the 750-hour threshold of material participation.As always, it's a good idea to consult with your CPA to ensure you meet the requirements and can take full advantage of the RE Pro status and the deductions available.

Have very good partners and find the best Architects and Engineers.

Good tip on the cost plus vs fixed price!

They must pay the market rate, the same rate you officially list for the property.The good news is that you staying in your STR for the purpose of making repairs is not personal use.