Windows redistributables are installed in each game’s Proton (Wine) prefix directory, not globally. However, I have seen an example of Proton continually forgetting that it had already installed .Net for a certain game, which turned out to be due to a registry entry not getting set during install. If you’ve found a situation like this, it’s probably worth reporting on the Proton issue for that game.
people are really big on flatpaks right now but avoided that due to issues with like the two native linux games that still exist in Steam (mostly joking).
I don’t know what issues you encountered, but if you’re interested in the Flatpak, it might be worth trying those games again, possibly with Steam Linux Runtime manually set in the game’s compatibility options. Recent runtime versions have changed how they provide libraries to native linux games.