So that means if I invest 252 EV into Attack, and give him say an Adamant Nature, Flail can be deadly? And do more than the 200 Damage?

You're still missing the point. Flail's base power increases the lower the user's HP is (max 200 BP). And base power doesn't equal the amount of HP damage done (Flail doesn't always inflict 200 HP damage; the damage it does is based on the damage formula posted above). Base power is just a number based on how powerful a move is, i.e. Surf has a base power of 95; Slash has a base power of 70, etc.

The only moves that inflict fixed amounts of damage are Sonicboom (which always inflicts 20 HP damage), Dragon Rage (which always inflicts 40 HP damage), Night Shade and Seismic Toss (which always inflict damage equal to the user's level; i.e. if a level 50 Pokemon uses the move, it always inflicts 50 HP damage).