Or is this a scenario where I might legitimately charge some small extra amount for the basement (such as for storage) - or otherwise just keep it locked off separately from the rest of the house?

They may charge you a small fee but it's worth it. 

What's a fair return we should pay him or what's fair for him to charge?

Do You Offer a Discount for Vendor Services or Do You Up-Charge?

@Drew AdamOnce you close, I would meet/talk to the tenants and let them know that you will need a new application (I would not charge them) and vet them like any new tenant.  

Most companies I've looked charge a % of the monthly (or weekly, etc.) rent.

I get info from REIN but the prices they charge compared to what you can get at REAG - hands down, I choose the latter.  

I get 2.5 points charged with each one of the two loans, I have no leverage to negotiate the 30Y mortgage rate, no closing credits and if I want to refinance with another lender in the market I'm charged a hefty fee that will make the other loan unattractive anyways.

It's not like a loan gets paid to the seller in installments over time or can be reversed like a credit card charge, once it's approved, the seller gets the full amount and it's sold, right?

There is a clear market limit as to how much rent you will be able to charge your tenants.This slide from the Feb 9, 2016 KnoxREIA monthly meeting shows the comparison of the Knoxville MSA to the Nashville MSA (information is from MetroStudy).