By Over Torqueing the Nut, it pushed the Flywheel further down the Taper on the Crankshaft. That would stretch the metal, and from then on the Flywheel would be a little Lower than it is supposed to be. You already say it has hit things below it that it should have cleared.
My Book doesn't show the 100 - 105 spec until 1960, when the slightly larger 40hp came out.
We had a 57 35hp, and later we had a 63 40hp. In 74, the 40hp was tuned up at a Dealer. I took it out the first time in 74 and 10 minutes later, at WOT, the Flywheel came loose. Fortunately the Recoil Starter above it prevented it from coming completely off. The Mechanic didn't torque the nut properly, or put it on, went for lunch and forgot to finish the job properly. I guess my Dad had a very one-sided conversation at the Dealership, where they were doing all the Listening