Some jokes have the side effect of making people feel welcome or unwelcome in the community. I'm not sure "toxic" is a productive word to use here, but the community can absolutely be a "boys club".
To take one example that stuck with me, I recently went through this Quake C
tutorials by MauveBib (from back in 2008? or earlier?). Between useful information, there are some of these "boys club" jokes that aren't very funny and also make me feel like an outsider. As a result, I'm wary to pass on an otherwise-useful tutorial to friends who might like modding in QC. I don't think the "humor" of these jokes makes up for the way they make people feel unwelcome.
My perspective in the quake community (as a comparatively recent arrival) is probably an odd one. I work as a professional level designer with a background in Unreal Tournament modding. Most of the professional level designers I know also got their start in mod scenes, which were also "boys clubs". As a result, we're kind of a samey lot, making samey games, and it's all a bit creatively-empty and dull. I like working with more diverse teams, which requires more diverse applicants, which I think means making the mod scenes more welcoming spaces so more people can gain those skills in the first place.
I also see a new generation of would-be level-designers learning in Unreal Engine and Unity outside the context of any specific game. They're learning the tools, but not the concepts, so it's not proper level design. When I've been involved with hiring LDs, the applications from game dev university graduates are terribly shallow. With those concerns in mind, I see how Quake and Trenchbroom could serve a new generation of level designers by providing them an environment to learn. I've tried inviting some friends with that hope, but they have bounced off after making a map, if they even get that far. Maybe I'm correct in the "boys club" diagnosis, or maybe it's inherent to Quake and a weakness of its theme and a narrow appeal?
In any case, with things like Quake 1.5 and weirder experiments, I think there's a productive way to say "cool, this isn't for me, but it is still welcome here". Per Baker's thread, I think it can also be useful to say "hey can we get more [x, y, z]", but I don't think it has to be either/or. We can have co-op maps and id1 maps and AD maps all at once without detracting from each other! I think there's also value in highlighting the work of newcomers, and creating mapping events specifically to welcome them and offer feedback. I've brought it up before, but Doom is a comparatively lively and diverse scene, and I think that's worth aiming for.