Or does it just get accepted as a matter of course, and then they audit you later if they want to? 

Communication, turnaround time, formatting, ease of audit, flexibility? 

(make sure you audit it and give it a peer review).

@Josh Deno If you are audited, you will need to show that you had the intent to hold the property for rental, investment, or use in a trade or business.

An attorney will never guarantee you can win at trial, a CPA will never guarantee you won't get audited and an inspector won't ever guarantee the house they just looked at won't fall apart.  

I've done audits of 401K plans in the past too.

An audited appraised value position will be provided to investors/lenders on a monthly basis or when changed. 

Ginnie Mae's Books Can't Be Audited

You would have to be able to demonstrate your intent should you get audited.

It's just good practice to have a dedicated bank account because, heaven forbid, if you ever get into a lawsuit and need to provide records, or you get a letter from uncle sam to audit you......Plus it'll save you time when you want to run the numbers to see how well you're doing on the property.