one other possibility, have you measured the voltage when running with the alt hooked up?
I had a bad connection to the VR one time and it vaporized an inch of 10 gauge wiring and melted about 2 inches of insulation on either side.

normally an alt will only put out as much as you need, so a dead short would be the normal way to blow the fusable link.

but as you already determined, it didn't blow with the car in run only, and it didn't blow with the alt removed.

it could be as surmised a bad alt that has an intermittent ground. Or it could be a bad charging system.
in my case it was a bad connector, and it caused a serious over charging condition. It was a long time ago, but I recall the guy saying it was putting out over 100 volts.
It was before I understood electrical and someone converted the car from the old 40 amp alt to 100 amps and the 2 field vr.
The connector they used was poorly crimped and not weather protected.

I would see what your voltage is while running and see if that could be a cause before swapping out alts.