I agree here with Matt.
You can't have too many confirmations before making major changes.
+1
I rely on this feature, honestly. With massive tagging changes (which can apply to the in-file tags and go "live" immediately), it is good to have a stop-gap to prevent accidental massive tagging changes. This comes in particularly handy in situations when, perhaps, you have the wrong panel or file-set selected and you try to make a Pane-tagging change. So, you expected the tagging change to only apply to a single file or three, or maybe a full album, but you'd accidentally selected an entire Artist, Genre, Series, or Media Sub Type. This warning flag "catches" those situations and prompts you to do a double-check. If you pre-expect a large tagging change, it is a small matter to just click Yes. As I mentioned, these changes are live immediately, and can actually be disk-intensive (and difficult to "cancel in place") if you accidentally apply them to a large file set. Undo can be a solution, but usually it is a multi-step process to get yourself "restored" (writing tagging changes back to the files and whatnot), and I've had situations where undo completely fails me (say you apply a big change, and then something goes haywire, and you need to shut MC down while those tagging changes are still in-progress before you can even attempt an Undo).
I'd need to actually trigger and look at the dialog to confirm (which I'm not going to do right now because I'm being insomniac and trying to walk away from bed for a short bit to reset), but doesn't it provide a "don't bother me about this again" checkbox?
If so, I think that is a reasonable setup and should be preserved. If not, then that checkbox is all that reasonably needs to be added, and I still think the current behavior is the most reasonable default.