Hacham-
It’s been a really long time since I’ve went over that sugya, but here’s what I have from memory.
The mishna is talking about b’oneis. It has nothing to do with kana’im pog’im bo.
In Moreh Nevuchim (towards the end of the third chelek where he talks abot the reasons for the mitzvos) the Rambam explains the halacha that since this bi’ah may cause a mamzer it comes with a pgam that will last forever and that is why the person has a status of a rodef. At first glance it would seem that he did not have the girsa of zechur. It would also seem that any ervah b’oneis would be included. Why did the mishna specify na’arah hame’urasah? Probably because the Torah uses that case in Parshas Vayezei. And from here one could also infer that the din rodef would last until ??? ????.
Kana’im Pog’im Bo has to be during the actual ma’aseh. I’ll look it up later but I’m sure about this.