Besides ebay not getting any money when you do a deal outside of it, the main issue is that you won't be covered by them if things go sour. No different than doing a deal with your neighbour to buy his old car for your kid.
As Pablo mentions though, if it didn't meet the reserve I would suspect the price was too high in the first place. Unless there is some reason you really want that computer, you could just move on to the next auction.