Which record deal?  His debut album came out in 2001, Room for Squares. 
It was Room for Squares which the record company took and changed the feel of most of the songs and that must have been 2001. I remember talking to David about him in 2002 where he made the comment "He has'nt suffered enough".  The "Message in a Bottle" tune I put on Burn Unit 1 was one I downloaded  somewhere in the 1999-2000 area. Also a song called "Victoria" I really liked but did not make the 1st CD

There were however not one, but 3 Indie releases by young John, beginning in 1995.  So, if you are referring to those or one of those, I stand very much corrected, he did have some true Indie in him at one time.  But, of course he ain't in any way Indie now, unless he were signed to Sub-Pop instead of Columbia; that might make him more "Indie"....
No I feel he is very much overated. The 1st concert I saw was with Nora Jones (2001 or 2002) and he was the headliner. A bunch of teeyboppers there that ignored Nora and started screaming like crazed Beatle fans clued me into the market he was drawing