I'd be more suspicious of an intermittant open or high-resistance short to ground, maybe even internal to the battery. I'd want to start by removing, cleaning, and reinstalling all the main connections, including the ground strap, and checking the battery terminals for looseness. Depending on the year of the car (I wish we knew), I might even change the battery out even if it tests good.
The other possibility would be that something is intermittantly creating a high resistance short to ground while the car is operating. Removing the fuses for all unnecessary circuits, and if that stops the problem replacing them one by one, might help find it, but it'd be a crapshoot.
Another option would be to hook an event recorder up to the charging ciiruit. It's possible that the intermittant is internal to the alternator.
By the way, OP, have you had an aftermarket audio system or security system installed? Or installed one yourself? Aftermarket lighting, or anything like that?