You’re confusing Proton with community efforts like Lutris. Proton is a package of technologies (Wine, DXVK, Vessel), not a configuration manager. Each individual game gets an identical, isolated runtime environment without any bespoke modifications except for downloading precompiled shaders (if available).
It’s certainly true that Proton has hardcoded quirk flags for specific applications, but these are exceptions which prove the rule – there are <200 of these compared with thousands of Verified status games. Almost always, Valve prefers to fix the upstream Wine/DXVK bug rather than hacking around it. Any hacks which Valve does ship are in the Proton source code, not per-game environment scripts.