I had mentioned on this question that the question comments is an inappropriate place to discuss meta issues. Charles replied that if it is an inappropriate place to discuss these issues, the original comment asking the OP to switch to community wiki is also out of place.
I feel that it is perfectly acceptable to post a comment on a question asking them to change to community wiki. If we instead posted the request in meta, there is no guarantee that the author would ever even see the post and have an opportunity to change it. Not to mention that meta would be filled with unnecessary "can you change this question to cw" requests.
I guess I would say that the difference between a comment asking the OP to switch to CW and a discussion on whether or not it should be CW is that the former directly relates to the question on hand while the latter has to do with site policies themselves.