From Strange Shapes' interview with Verheiden:
QuoteSS: The series was a great success, and the way that characters like Newt and Hicks were handled was superb. However, after Alien 3 the comics were retrofitted to suit the canon of that movie. Hicks became 'Wilks', and Newt became 'Billie'. Do you feel that this recasting detracted from the series?
MV: Dark Horse felt they needed to make those changes so the books would fit into the Aliens film canon post Alien 3. It kept the books in print and I happily cashed my royalty checks, but I had absolutely nothing to do with the re-edit and as far as I'm concerned the original stories are the ones I would prefer for people to read.
https://alienseries.wordpress.com/2013/02/21/strange-shapes-interviews-mark-verheiden/At the time they were releasing/re-releasing a lot of the comics as trade paperbacks and decided to take the opportunity to modify them.
(Interestingly he also notes that they weren't allowed to have Ripley in it originally for licensing issues, which says a lot about how seriously Fox considered it any sort of official continuation of the series at the time. Verheiden
also mentions that comic tie-ins of movie franchises were the bastard children of the comic industry at the time.)
So as I've said from the beginning, no: that A3 ignored the comics is not the same as this movie (very potentially) ignoring A3.