It can be a huge pain to get started but you do get your rent direct deposit every month.

I also let him know that I would need 3 months of bank statements showing deposits going into his account from the business.

And this is CRE, so it's cutthroat, it's no one's problem but your own if you lose an earnest money deposit. 

Should I speak to my lender first and see if they can match?

So, if you can't match whatever is already in the kitchen, then I highly recommend you do kitchen and dining area.  

Others will collect first, last, and a smaller deposit.

If a buyer is coming down with a high-down payment and quickly making a large deposit into escrow fighting tooth and nail about proof of funds may be a red herring.Credibility is also a factor here.

So the total amount that should be paid will be rent for remaining days in month + security depositORrent for remaining days in month + next month + deposit - I don't know when would this situation arise.

I'll reach out to the lawyer in the meantime, but I suspect if they refuse to pay it, it'll have to come out of their security deposits when they move out?

At a bare minimum, I would require a written lease agreement and a standard security deposit equal to an entire month of rent.