I had indeed read and understood the earlier comment that you linked.
I just got confused by your “user error” suggestion, because I don’t see how this qualifies as one.
First, the Reddit API is broken, because the select query sent by the deletion tool receives less than a full set (as if there was an implied LIMIT clause on the server side). This leads the deletion tool to erroneously announce it has processed all comments.
Two, the Reddit UX is broken, because the profile’s Comments page incorrectly returns an empty set due to a silent design limitation (as described in the linked comment).
There is literally no mechanism to find leftover comments through either the Reddit API or UX, because both are broken. The only workaround is to use a search engine that had indexed those leftover comments.
That’s the whole point of my original post, and I don’t see where the “user error” may come in.