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You know how it goes - change these things and you get even louder complaints. The assumption when implementing it like this probably was that it is likely that these flags need to persist across interrupted game sessions but the multiplayer relevant dmflags don't.

I would expect them all to behave consistently - either they all save or they don't. Got caught in the situation OP describe a few times myself - was playing some old WADs with compatibility, then forgot to turn them off for playing modern WADs.

What makes you think this is a *bug*?

DMFlags are always reset every time you load up GZDoom. CompatFlags, however, do not. This often causes issues when one manually sets specific CompatFlags to play WADs designed for vanilla, for example, but as one would assume that CompatFlags are reset much like DMFlags, they unknowingly play newer wads with those flags carried over instead, sometimes leading to unintentional behaviour and bugs. The player should be right to assume that DMFlags and CompatFlags are standardised in how they both reset with each new instance of GZDoom.