You can handwave that after the fact, but there's no way that was their intent when they filmed the scene, or he would've said something about it in dialogue. That's what's so bizarre about all this. Why did they change their minds?
It barely requires any handwaving though. It's a hologram of a dying man, it doesn't require a line to explain everything, the audience can fill in the gaps. But I understand where you are coming from, there are clearly inconsistencies within the text and in some of the supplementary material on social media.
Jack's stated age of 24-25
Is this actually stated? I know we had Picard speculating that he was 23 or 24, which Jack neither confirmed nor denied. I may have missed a line.
Again I don't think this is a smoking gun. She was made acting captain of the Stargazer at the end of season 2, which, with the backing of Picard and Janeway, may easily have become a permanent rank given her relevant experience.
We saw Kira commissioned as a Commander, the Maquis were given provisional ranks which lead to Captain Chakotay, Kelvin Pike did whatever he liked with Cadet Kirk, and there's whatever happened with First Officer Tilly. Starfleet is pretty flexible with handing out ranks and promotions. Unless your name is Harry Kim.
This season was obviously written and filmed with the assumption that it took place sometime later, and then for some reason they changed their minds and pushed it back to 2401 despite the discrepancies that creates.
I don't disagree, but I just don't think it's particularly problematic. If they did screw up, they seem to have caught pretty much everything by the time it was broadcast.
As you say above (whilst I was typing!) these things happen during production. There's lots of moving parts between scripting, design, filming, post-production. They won't ever catch everything. So far I'd say they've done a pretty good job at reconciling it all.