It doesn't get confused but it can change the feeding for specific MB's.

The main reason why it is disabled in tournament play is because that mech can be problematic sometimes with registering hits. I'm sure TD's would rather disable it vs having to argue "that's pinball" with a bunch of people complaining that they didn't get a lock because it didn't register or catch the ball.

If you have lock lit and the hammer doesn't catch it to lock the ball, until it finally does so, all additional hits to the captive ball don't count towards your next lock. It can be a big road block to Coffin Multiball.

Avatar it is because the powerball is random and it doubles scoring. Tournament play likes to remove the randomness of awards so the games are decided more on skill and less on luck.

I believe this was changed in a code update...the hits to the hammer do continue to count even if you have not locked a ball. I've had all 3 locks lit and locked them all one right after the other. It is still different locking balls, sometimes it grabs them with a slow roller and sometimes it takes a real slam or a hit to a target or the snake before it grabs.
Another reason that some TD might disable hammer in tourney is because if 1 player has a ball locked in the coffin, then the 2nd player locks a ball it will kick out of the mystery scoop instead of the shooter lane, so it can be confusing to players who aren't ready for the kickout from the scoop. Alot of times the kickout from the scoop is harder to control than a ball served in from the shooter lane.

Phoebe