Hi, based on what you report, which seems to be that the starter continues to make a noise AFTER you release the key when the engine starts, the continued noise from the starter may be due to it having already been damaged by the improper installation, or the mechanic still has not shimmed it properly and it continues to hang up.
As for the missing flywheel tooth, that would NOT be the reason for the noise from the starter, as it would more likely let the starter gear release rather than hold it in. A missing tooth is not necessarily a disaster unless the starter attempts to engage at the broken tooth, in which case it may not be able to, depending on how much of the tooth is gone. So what you end up with is that the engine may not start since the starter cannot engage what is not there, or that while cranking, the starter may disengage at that point, depending on remaining material of tooth on flywheel and condition of adjacent teeth.
If you never had a problem with starting and now you do, I suppose you could argue that the damage was done by the new starter. I think the mechanic will argue with you that it was preexisting, mainly because it is a big job to replace the flywheel gear.
A good mechanic should be able to recognise the starter hanging up and install the proper amount of shims , and I have to wonder why he did not in the first place.
The amount of shims can vary in order to make for the proper alignment, and sometimes it is the difference of a few thousandth of an inch between proper lash and hanging up. Although shimming is not mentioned in the following articles, it is a generally accepted practice with this starter design.
1993 Isuzu Truck Trooper (4 Door) V6-3165cc 3.2L DOHC (6VD1)
Vehicle Level 
Starting and Charging Starting System 
Description and Operation 
Description and OperationThe starting motor has field coils mounted in the starting motor (yoke) frame. The magnetic switch assembly and the parts in the starting motor are enclosed in housings so that they will be protected from dirt and water. In the circuit, the magnetic (motor) switch coils are magnetized when the
ignition switch is closed. The resulting plunger and pinion clutch movement causes the pinion to engage the flywheel gear and the magnetic switch main contacts to close, allowing cranking to take place. When the engine starts, the pinion overrunning clutch protects the armature from excessive speed until the switch is opened, at which time the pinion will disengage.
1993 Isuzu Truck Trooper (4 Door) V6-3165cc 3.2L DOHC (6VD1)
Vehicle Level Starting and Charging Starting System Testing and Inspection Pinion Gear Does Not Properly Engage Ring Gear Pinion Gear Does Not Properly Engage Ring Gear
Testing and Inspection Fig. 1 Pinion Gear-ring Engagement Is Improper.
I hope this info helps give you some frame of reference. Good luck.