I doubt anyone can give a 100% answer. It may hold forever or it could take off. If you can catch it with your fingernail it's most likely too deep to polish out.
I have two scratches that deep in my 41gl rimless however that glass is 3/8" thick. My has held water for 10mos.
If it's in the budget you might consider removing it and replacing that pain. Also since you plan on painting, you could substitute smoked glass for that pain.
Just a +1 on the first sentence.
From my perspective, the very bottom of the lower scratch in third picture doesn't look promising at all. It looks like it's already telegraphed to the back of the panel. Could hold for a decade, could run edge-to-edge when you fill it the fourth time. A rare occasion when I would recommend doing it over. It would also give you the opportunity to do a better job with the outer beads as well. With tape on either side of those beads and a convex shaping tool, you may gain some peace of mind and some neater outer silicone beads.
The paint dept. of the box stores all carry some form of tool used to shape caulk lines and are dirt cheap and perfect for the job. You can also shape the edge of an old credit card for the same purpose.