I know banks want to see reported taxable income and I don’t want to cause any red flags or have IRS get involved.

It looks like the certification process may be a self-certification form filed with your taxes..Not too much red tape involved!

Is that a red flag for lenders?

Strawman, attribution, proof by assertion, Red Herring, and cherry picking. 

Bank A may promises better rates and terms, but if they haven't been able to close on a single self storage deal in the past year, that raises red flags for me.

Living on a boat and working for $12 an hour is a pretty big red flag for me.

The charity and compassion arguments are irrelevant red herrings. 

as your primary you should be able to get an O/O HELOC my guess on the move out question would be dont ask dont tell, so residential HELOC's tend to be 10 year term, so I would maybe get the HELOC from a bank you dont do investing related banking with maybe an out of area bank or bigger institution. and set up a P.O. box or a different address to get correspondence from them (totally reasonable in a multifamily) this way when you move that doesnt change, so no red flag for them to call it due.

You have the red flag already...."

There are many red flag involved in your initial post.