The first thing to remember is that comments exist almost exclusively to point out problems with the post. The author then hopefully edits accordingly, then the comments are deleted. The main point being that comments are meant to be deleted eventually.
However, on this site and many other SE sites there exists a convention to leave comments that are "related" to the topic, or "interesting and relevant". Prime examples on this site are opposite questions being linked in comments ("What is the basis for belief X?" contains a comment to the question "What is the basis for belief NOT X?").
With that in mind, we have ourselves a broad gray line between doctrinal debates and "related" and "interesting and relevant" comments. If there is a legitimate question on the site that is related to the topic, even in the way you describe, feel free to link it in a comment on that post. That seems perfectly reasonable. Something like "Adherents to Yism believe that Xism followers misrepresent their views. See ..." It seems a very benign comment and it's backed up with a link to another post. Readers can click through or move on with their lives.
But if you get a reply along the lines of "Actually, no, Yism is a cult and they're liars" or whatever, you're only reply should be "We shouldn't debate the pros and cons of Yism here. We can go to chat if you like. Also, if you think the answers on the post about Yism are lacking, you should offer up a new answer or comment on the existing answers. This post is about Xism."