CoC1 kinda got put in a similar position. The game was distributed all over the place, and there was no real way to control it, so in a bunch of places the game with a bunch of stuff the devs didn't really want to be associated with was being linked directly to them.
At least in regards to /hgg/ mod (which I believe had the most extreme content?), it would be pretty hard to mistake it for a vanilla release I think. Could be even clearer by just having a marker that shows below where the author name currently in coc2, explicitly stating a scene is modded or unofficial content.
Better mod support would stop people from needing to create new versions of the game to distribute anyway. Nobody is uploading and sharing modded skyrim installs, you just pick the mods you want from nexus (or lists via wabbajack). Monster girl dreams has a similar approach that works fine.
Bug reports would be annoying still for sure, but there's no way around some users being fucking morons and submitting less than useless reports. Some "people" can barely read a few posts above theirs before asking a question in a thread here, there's just no cure for brains that smoothly polished. More seriously, reports being low priority unless a save is uploaded fixes a lot of that I think.
Wanting complete creative control is the only real reason to be entirely against mods here, I think. Only one that doesn't either make them look lazy or fall apart under any critique at least.
I'm surprised they didn't include a spite option 'well, since you never met any of our obviously fabulous characters you stick a finger in your butt and watch the dragon die' if you ignore both the hornet dickgirl and dom dickgirl.
Where's the spite though? That would be objectively the best choice. No bugs, evelyn stays sitting in her room like a loser, and you get to (kinda) kill a dragon.