At 1% you’re really not making much once you value your time and long term maintenance on a home.

Low maintenance & good tenant. 

Anything left over after paying bills should be transferred to savings.Savings: set aside funds for CAPEX, maintenance, PM, taxes, insurance, or whatever else you planned for.

Granted, I am relatively new to the small commercial buildings, and my experience has been in the residential, where things are relatively easier.To clarify a few points, the management company have their own maintenance teams as well, so it's not a function of them stalling services because they don't make money.

Debt to ratio is okay and already have 3 renters in apartments and occupied .The question I have is, how common is a letter of explanation with loan process ?

Is it common place for non-agents to write up a "referral contract" to collect a similar commission that would be due to a broker?   

Protection of assets is commonly cited as a reason for holding investment properties in a company, however what protection does this provide since the bank still has a mortgage over the title?

Yes it’s very common and done the exact same way as residential.

This implies the $200/month cash flow in unlikely to ever be worth more than the $200.I recommend all investors start local but you seem to be adverse to that so I will go with another one of my common assertions: The only Midwest investing that makes sense for most Coastal So Cal/San Fran RE investors is true MF (5+ units).  

[Lenders commonly use 70% LTV for investment loans].eg.