Looks good, nice work!
It is common for tempered glass, even basic float, to show some wavyness like that. I have seen it often in my years of glass work. Nothing to worry about. The glass is quite thin, heat treating to temper it could contribute to that as well. It is structurally sound.
As for the sealant, first and foremost NO silicone!
I would get a tube of Dicor non sagging. There is self leveling, which will flow and run out. There is non leveling, which is more suited for vertical areas. Clean up the old stuff thoroughly before applying. Wipe the area down with a bit of acetone to clean it.
But caution, only a light wipe if you use acetone. It will remove paint.
If you caulk it when it is cooler out, there is less chance of it sagging.