Generally when I flag a comment as "no longer needed", it's a response to a removed comment or a request for an edit that has been made. It's a bit strange to have this option right next to "this contains bigotry, etc". In addition, flagging a comment suggests something more serious than it is, which probably shows the incorrect level of urgency to anyone reviewing. Is there something else that I should be doing to these comments?
TL;DR: Flagging is the exact right thing! No, I don't think we need something different. Maybe we could look into changing the toast notice when you flag as NLN to make it less serious but it seems like a small issue.
Coming up on two years ago (late July 2018), we made a pretty major change to the comment flagging dialogue. You can see what it initially looked like after the change in the answers here and it changed a few days later to what it currently looks like. Up until that time, the disparity between rude or abusive and no longer needed was larger as the "unfriendly" reason didn't exist.
It may seem silly to point out but, "No longer needed" isn't right next to the harassment reason. It's got the unfriendly reason between the two making a gradual transition between blatantly abusive and simply not necessary and you don't even mention it in your question! This is intentional and helpful. And at the bottom, the other reason can be used for all sorts of things from "This entire chain of comments is chatty and should be moved to chat" and "Please burn this chain of comments with fire."
This is when we added the confirmation toast notice - which I think we tested a few wordings on. The text is designed for the more serious flagging reasons but I don't think it's so severe that it should give you pause. I handled thousands of NLN flags (before this change) as a moderator and I did take them quite seriously... I deleted almost every comment.
So, I guess we could look at changing the toast notice text to something that feels less serious but... I think there's a lot of other things that are more important for us to work on and I don't really think the benefit would be that large. Heck, when we created it, all people wanted was for us to make it go away or at least make it less visible.
In the grand scheme of things, we have a hugely complex system that is underused as it is. We get support emails from people about rude content on the site rather than flags all the time so making flagging more complicated or adding a different type of mechanic for obsolete comments is just reducing the likelihood that someone will even use the tools at all.
I accept that it may seem confusing to some people and I hope that familiarity will help get past that - flagging is the correct thing for these comments and please don't let any cognitive dissonance get in the way of you using flags to bring these comments to mods' attention.
We do actually treat these flags differently, by the way. A user with several comments flagged as harassment or unfriendly in a short period of time where the flags are all marked helpful (three in a week) will get an additional flag raised against them by the system asking the moderators to look more closely at the user. This doesn't happen for NLN or moderator attention flags, which have no impact on the user at all.