You didn't say if the marina did the alignment while the boat was in the water although it sounds like it was done while your boat was pulled. If that was the case the mech. wasn't to swift since you will almost never get a good engine alingment while the boat is on "the hard". As stated earlier fiberglass boats will "twist" to a certian extent when blocked up. For proper alingment the boat must be put back in the water for at least a couple of days so the hull can "relax" back to its natural posture, then they can aligne the engines properly.
I wouldn't pay until the job is right, but as for the estimates it is buyer beware since most states don't give the same protection to boaters that covers auto owners when it comes to repairs exceeding estimates. Always get an estimate in writing and spell out exactly what work is to be performed and the exact cost. Also include a provision in your estimate for the mech. to get prior approval from you if repairs are to exceed the quote by more than 10 percent.
1999, 52' Monticello - Miller Tyme
Port of Aurora IN