Yes, every time I see it I have to look carefully to be sure it means what I think it means, because it's so commonly misused.

We want to make a decision when @tkoeppe is present.

Personal opinion: I think "comprise!" is exactly what we want to say here, popular misuses notwithstanding. We could consider adding an entry to our "terms an definitions" for this, to avoid any doubt about local use.

I'm sympathetic to the concerns about widespread misunderstanding of "comprise" (and I checked a couple of online dictionaries, which seem to list both the "correct" definition and the colloquial/"wrong" one); I generally prefer descriptive linguistics over prescriptive linguistics, and if popular usage is ambiguous, then we should look for a more-precise term. If our words confuse reasonable readers who are paying attention, that's a bug even if the words are technically correct.

That said, in formal, technical writing such as this, I think the expectations on usage lag significantly behind the vernacular (for example, we almost entirely eschew contractions), and the historically-correct interpretation should generally be understood as the intended one. When we say "literally", we don't mean "figuratively", and when we say "comprises", we mean "is composed exclusively of", not "form part or all of".

I don't think this is an easy choice. If we can find a good alternative that doesn't sacrifice clarity for the readers who are correctly interpreting the existing "comprise"s, I think that's worth pursuing, but I suspect any alternative here will be at least a little more verbose and/or less clear.

Well, I think "consist of" is a synonym that works in all cases (modulo appropriate declensions) and addresses the concern. Since there aren't too many uses of "comprise" yet, making the change at this time seems relatively painless to me.

Editorial meeting: We found some misuses; fix those. Use "consists of" mostly, except where "comprises" cannot be misunderstood.