I'm not sure there's a problem. The message is "please consider adding a comment if you think this post can be improved". What's the circumstance under which it's inappropriate to comment if you think a post can be improved? If you don't think a post can be improved, this isn't telling you to comment.
Beyond that, it's important to consider that one might downvote or upvote posts on meta for the same reasons as on main, as well as for other reasons. All the reasons to upvote or downvote on main apply on meta; it's just that there are some additional meanings associated with votes on meta that don't apply on main. If you think a question shows poor effort, or that a question or answer is unclear, or that an answer is factually wrong, these are all reasons to downvote. If you think a meta post is good, that is still often a reason to upvote. So the message suggesting that meta users consider commenting is still applicable, even though there are many situations where a downvote doesn't express that there's anything wrong with the post and thus doesn't suggest that the post should be improved.
This is related to what I would consider to be a much more serious matter of confusion: the alt text (i.e., tooltip text) that appears when you hover the mouse pointer over the upvote and downvote buttons on meta is the same as on main. This causes many users who are new to meta to feel that they (or others) have been unfairly downvoted, and slightly steepens the meta learning curve.
There's a bug question for that on Meta.SO. The votes seem to show community consensus that some kind of change or addition should be made to the meta vote arrows' alt texts...but it is tagged status-declined. Jeff Atwood's post explains why, but other members of the community have suggested what appear to be reasonable middle grounds.
In any case, since that bug report / feature request was denied on Meta.SO, and since the behavior of tooltips is (at least with the current implementation) a network-wide behavior and not site-specific, it seems unlikely that this feature request will be granted. It's still worthwhile to request the change if you think it ought to be made, of course.