The problem is blistering (osmosis) and is usually an issue with the gel coat and process the manufacturer uses. It is not unusual and most often happens to boats that stay in the water all season. I had a boat (manufacturer withheld) that had severe blistering. Under the 5 year hull warranty, the manufacturer redid the bottom and extended the warranty. Not sure what Rinker's warranty is, but it sounds like its out of warranty. It's not necessarily a major problem. Here are a couple of links that give more info.
http://www.nsc.ca/nsc_library/techtalk/osmosis.htm
http://www.boatus.com/goodoldboat/blisterbottom.asp
The fiberglass shop across from Faye's (Bill Amadon) did the bottom on my last boat and it came out great. The manufacturer actually came out and certified them so the boat didn't have to go back to the factory for the work.
$2,500 sounds about right to have the bottom re-done. If you're getting a good deal on the boat, and have a competent shop do the work, you're probably OK.
I'd definitely check with Bill. Good luck.