I can't count the number of times that I've seen a post from a well-intended, albeit naive, questioner get the comments section of their post (which can't be down-voted) hijacked by people who get pleasure from patting each other on the back for being smarter than the questioner. And, on the way out, down-vote the question only because it insults their intelligence.
I can't count the number of times a user came here with the same unclear request about how the community has been mean to them in the comment section.
Let's get something straight, Well-Intended is not what makes a post valid for the website. We all get our first post downvoted badly or get a bad reception when we start here because there are rules that we must follow in order to get a proper collection of good questions and answers running. When this happens you have two choices, learn to fit in and read the help center to ask better posts and improve with the time in order to help other users. Or be against the whole thing, come here on meta, thinking of being the first one to post a non well received question by the community and whine about it thinking the whole system will change.
If all the users took the time to read the help center and the guidelines before posting, we wouldn't be having this discussion.
Now as for the questions which are btw kind of unclear.
I've never used the flag feature. But, does flagging a comment as unproductive work to deincentivise the user who posts the unproductive message?
I'm no Stack Exchange developer but I'm pretty sure collecting flags like you would collect the hats is not a good thing. A flag collector will, one day, hit a wall. (get banned)
Why should user's be limited to only 10? I've seen comment sections long enough to use up most of that allowance.
10 flags limit? It's to limit flag abuses. We don't want to fill up the flag review queue with users that are unhappy with the reception of their bad "code this for me plz" posts and that decided to flag every comments below.
If the user has a score of, say, 100K, are they innoculated from anything other than flagrantly disrespectful comments?
I'm sorry but I don't even understand that question.