I'd also be interested in Craig Kyle's response, should he reply.
1) I'm with you on excessive retcons, but this is more of a remix, as it's using what is there and just adjusting it, rather than adding something huge, IMO.
2) This is the nature of working for hire, and I'd rather have Laura continue to develop than be frozen in amber. Also, Laura has always been a somewhat confusing creation in terms of science/comic book science, with "clone" & "genetic duplicate" causing some confusion and scientific consternation, so clearing that up isn't necessarily a bad thing.
3) I think this is quite an arbitrary distinction you're making, but by refocusing Laura's perception of her mother it certainly provides more story potential. Laura's Aunt and Sister might have something to say on this too!
4) I'm certain that Anka and Rowell have avoided the Runaways TV show to avoid it influencing their story, and I'm not sure that this applies with regards to the XCU and the current comics. Not being dismissive, but wanted to clarify that point.
5) Laura's discomfort with being a clone has already been explored, now she has a new self-perception to reconcile, which is fascinating. It's not a strong suit of her previously, and she's been really clone-positive with Gabby, and now that's gone.
6) Any character in comics for long enough will have their eyes coloured incorrectly at some point haha, but I do like the tidiness of it explaining Laura's eye colour here.