By far, by very very far, the best way to cope with a short sale is to build all the possible variables into your offer. Use this case as a learning process. In your next short sale offer, make sure you build in a credit for non recurring closing costs, recurring closing costs, and repairs into the original offer. That way it will be included in the HUD that the listing agent delivers with the short sale package. Even though you don’t do any diligence prior to submitting the offer at least you will have some built in cash back. Now by doing this of course you may (will) weaken your offer but at least you will not be quibbling over a few thousand dollars on the purchase of a home worth hundreds of thousands of dollars.
If you are making an offer on a short sale and you are coming in like 20% down I would advise not to weaken the offer in such a manner. However if you are coming in fairly close to the asking price AND there are no competing offers, then yeah go ahead and build it into the offer.
The worst thing as a buyer that you can do to your chances with a short sale is to change things up, which then require another HUD (most of the time) and then throws a wrench into the process. It essentially gives already overburdened loss mitigation departments more excuses for more delays.
