Best way to seal old solar panel screw holes?

Hi folks,
I have a 2019 Boondock T@G. The old factory solar panel failed and I need to replace it. Unfortunately, it was installed by drilling directly into the roof.
Before I put a new panel up, I want to seal the holes permanently. Filling them with sealant is the quickest solution, but I won't be able to check or reseal them without ripping off the new panel.
I'm also planning on repainting the whole roof, so I'd like to do a permanent repair that can be painted over.
Has anyone done a repair like this or have any advice? I believe the roof is aluminum instead of fiberglass, so I was thinking of filling inside of the holes with some kind of sealant, and then over top using Bondo Metal Reinforced Filler. 

2019 Boondock Edge T@G