At the first linked question, at the time of writing there are only two deleted comments (on the question, no deleted comments at either of the answers [of which one is deleted and only visible to 10k users]). Both of these were deleted by their respective authors. That left one comment there hanging without connection to anything. That should probably be deleted now.
At the second linked question, I have yesterday deleted a number of obsolete comments (requests for clarification that were then incorporated in the question and confirmations by the question author responding to those, responses to comments that were deleted by their authors) since the comment thread became very long (and we got a user flag asking for clean-up in addition to the system flag). Of the thirty comments deleted at that question, if I have not miscounted, fifteen have been deleted by the comment author, and fifteen by me.
I tried to leave the thread in a state that makes sense, but without deleting the whole thread, there had to remain some oddities.
When comments become obsolete, deleting them does no harm, and if they are numerous enough, deleting them is beneficial because it makes the non-obsolete comments more visible. Hence obsolete comments are likely to be removed when our attention is brought to them by a flag.