OK, this is how I read it:
There are many opinions. If Cav only won because the others backed off then it's not a real win and he hasn't really broken the record. He only wins if he is the fastest rider. End of story. So. Is there a prologue/time trial* for next years TdF? (ironic question) If so, would a victory in that count as a stage win and so count towards the record? Cavendish lives on the IoM.
*It's actually a fair question worth asking! Prologues are not an official stage so a win in one may not count as a stage win! I genuinely don't know... But it does point to a silliness about the arbitrary nature of some records. That is, what does and doesn't count towards it.
Following on, FWIW, I don't think many people consider this particular record to be anything more than a count up. There's little of greater relevance to it, let's put it that way. Everyone is at pains to point out there is little or no comparison between the 2 riders. They are different riders; apples and oranges. So to suggest anything on the basis of this record is foolish.
I think the stage win mattered more to Cavendish than the record. I'm hoping he forgets about it. I'd go further, I actually kind of hope he retires now.... well, I'd understand it if he did and think it a good decision. He has nothing left to prove. He will be spoken of as the best sprinter of the generation, if not all time. Nothing that happens next year will change that. But, personally speaking, I'm not so sure he'll get a ride next year, it'll depend on his form before the tour. This tour has been magical for him, particularly considering the last few years he's had what with illness and injury. It would be an excellent way to finish his career.... IF he can come to terms with finishing it. For any athlete, it must be a monumentally tough call to make.