I think you may have posted the wrong link (10k users can still see deleted answers and that question doesn't have any) but what you've done in general sounds good to me because:
By posting a comment it gives the user a chance while they're still around to post their question and delete their answer (although that doesn't seem to happen in most cases).
The flag brings it to the attention of users who can handle it. The not an answer flag causes the question to end up on the low-quality queue where a combination of six 10k users, three 20k users or a single diamond moderator can decide to delete it.
Flagging a question as duplicate, off-topic, too broad etc will put it in the close vote queue where five 3k users (or a single moderator) can vote to close the question. For new questions there might not be a lot of point when it has a lot of eyeballs on it, but some older questions might no longer be answerable because of broken links / images etc.
An exception to this arrangement are the spam / offensive flags. Those don't go into a regular queue (diamond moderators can see them) but they give the post an implicit downvote and a total of six flags will delete a post. The idea being that enough fairly low rep (15+) users should be able to delete some of the really obvious crap as fast as possible.
The moderation on EE.SE both by the community and elected moderators is very good so in my opinion keep those flags coming. I saw a counter example a month or so ago on another SE site where when a diamond moderator hadn't been around for a day the front page was littered with junk and the community wasn't dealing with it properly. One example was a death threat against an entire country because of their religious beliefs being closed as "unclear what you're asking" when it clearly should have just been an offensive flag and outright deleted.