Nah I think HTML comments are fine. I don't think there would be a benefit to allowing comments in more places and it would make it more annoying when you actually do want to process comments.

If CSS had mandated that comments could only appear in certain places (e.g. before a rule or attribute) I think that would have been fine too, though maybe slightly confusing given the resemblance to C-style comments which are allowed almost anywhere.

Seems like we have broadly-similar perspectives, though I do find it a bit incongruent that the DOM preserves comments while the CSSOM doesn't. It feels like they ought to be in alignment one way or the other (though I also understand the historical reasons why they aren't).