I agree, for a $5630 flooring job the contractor is definately not going to quibble about a $130 difference to get to the even $5500 and of you potentially losing that money. But even if he's not, I would still put that money in. If it falls through the current owners will be out $5500 for that, correct? Their certainly not going to put materials you have helped to pay for into the house if you don't get it. Everything with home buying is paper work, should something happen and the house does not become yours you want your money back if a) the materials are returned or b) they put materials your money has bought into a house that no won't be yours.

So long and short, see if you can get it done for $5500, if not, make sure you get your money should something happen (which I doubt, but I know it's stressful nonetheless)