I'd ask a mortgage lender I know but I know his exact words, "There are too many unknown variables for me to answer that question properly."
If this is an in-house underwriter, I'd ask to sit down with the underwriter, your loan officer, and the president of the company (if that's possible) to talk about it.
It would seem to me they would at least base it on the lowest of the incomes - that is, unless they're hoping to convince you to go with a larger mortgage (which translate to more expensive home and higher mortgage payments for you) down the road so they're refusing you now but want you back in the future - I'm just thinking wildly here.
You really need to work it out with them as I don't know all the parameters. Remember, they're also not the only lender in town - you CAN shop around for a mortgage - just be careful with discount points and origination fees - some companies don't charge for these.
Prison, eh? Now that IS job security...the way it's going, it'll probably be easier to lock up and protect the innocent and let the bad guys (and gals) run loose.