Pre: Defo disagree that his range for continuing to a tree bet is gonna be this tight. Unless you have some sorta reason to believe this, like an ultra high fold to 3 bet over a good sample then you can expect a guy like this to come a long with a much wider range including stuff like 99 TT JJ AQ, maybe even other broadways. The gap between vpipand pfr is generally a sign of a villain being too passive and stationy so I'd 3-bet for value here very happily and expect to get called by a lot worse.

Flop: Yeah flatting here is going to be fine. Raising for value and getting it in is likely not horrible, but you wont be in amazing shape vs his continuing range and without a read of what he's likely to continue with (i.e 88? 6x?) It's probably better to flat and keep his weaker hands in. I wouldn't assume this player's actually thinking enough to check back all pocket pairs lower than 99, they could well be in his c beting range aswell.

Turn - Again, I wouldn't make his range this tight. This bet sizing is pretty weak looking on a drawy board and I'd expect most villains like this guy to blast strong overpairs and maybe even 9x harder to protect or whatever. Raising the turn, however, looks super strong and again without knowing how stationy he is, flatting is likely better and defo still +EV.

River - Meh, just fold now. Like you say he defo has all 9x, flushes, KK AA, maybe even AK KQ sometimes, although passive tards like to check rivers in these spots. Can't assume this guy's just blasting off 3 here unless he's aggro or bluffy etc.