Munchkinism aside, I see no reason for flurry to stack with two-weapon feats.
Flurry gives two extra attacks at high attack bonus, which is substantially better (in my opinion) than the two-weapon feats. Consider a 20th level monk, his flurry attacks are:
+15/+15/+15/+10/+5 with full STR bonus, or 1.5x STR bonus using Monk weapon two-handed (more on this later)
Compare that to using two-weapon fighting only, say with the full feat chain (Two-Weapon Fighting, Improved TWF, Greater TWF) and Monk BAB of +15 at 20th level assuming a light off-hand weapon:
+13/+8/+3 with full STR bonus, and
+13/+8/+3 with 0.5 STR bonus
Flurry is much better. You miss out on one attack, but all your attacks have +2 better chance to hit. Now as you're a Monk, you could use that to Power Attack .
Flurry specifies that the Monk must be unarmored, which probably means you can't use a shield, though it's not specifically stated (is a shield armor?). It doesn't say that you can't use your special Monk weapon two-handed, so here's the munchkin scenario that I would allow:
+15/+15/+15/+10/+5 with 1.5x STR bonus and Monk weapon, and Power Attack giving you +2 damage for every -1 to hit. So the best case same attack bonus scenario compared to the two-weapon chain of feats is:
+13/+13/+13/+8/+3 with +4 damage Power Attack on a d6 weapon. (Assume the weapon is Quarterstaff to avoid spending an Exotic Weapon feat.)
I think this last scenario is much better than two-weapon feat chains for a Monk. The Monk can spend his feats on Weapon Focus, Power Attack, Improved Critical, Improved Grapple, etc.
I'd be tempted to take 4 levels in Fighter to get Specialization for +2 damage in that Monk weapon, and Fighter 4/Monk 16 has BAB +16, so one extra attack too:
+16/+16/+16/+11/+6/+1
There's no way I as a DM want flurry stacking with two-weapon feats, way too many attacks and overpowered in some situations.