What we saw in Apocalypse wasn't the Phoenix Force.
It's not a retcon, because it's not said, in Apocalypse or Dark Phoenix, that this power we saw at the end of Apocalypse was the Phoenix Force.
Rather, it's a transition/climax scene of sorts which serves two purposes:
- establish how powerful Jean is currently
- plant the seeds for the upcoming Dark Phoenix movie.
Jean wrecked Apocalypse with her own powers
It's stated repeatedly in Apocalypse that Jean is even more powerful than she thinks, and that when she comes to realize it, she'll be able to do "whatever she sets her mind to".
That's what happens at the end of the movie: it's Jean embracing her powers, unleashing them upon Apocalypse, but really it's Jean's powers. Not an alternate personality, not yet a cosmic force, it's Jean. I went a bit more into details of this power and her self-control in my answer to How much self-control does Jean Grey have? on SFF.
But, that certainly looked like the Phoenix Force?
Yes, absolutely it did. That's because Jean has what I call "Phoenix traits" - namely, while she wasn't the Phoenix yet, she shared some features with it, which is why she was chosen to be its receptacle.
To me it looks like the fire wings she got at the end of the movie were a callback to her astral avatar from the comics; from her entry on Marvel's website:
When Xavier introduced young Jean to the astral plane a part of her mind manifested as a Phoenix raptor.
Like I argued in an answer to Is The Phoenix part of Jean's mind or a separate entity? (still on SFF), combine Phoenix avatar + borderline infinite powers to begin with, and you get why Jean got chosen as the Phoenix's host (but once again, was not the Phoenix in Apocalypse).
Going by memory, Jessica Chastain's character in Dark Phoenix even said something along the lines of
Many people tried to master the Phoenix but never achieved it, but with you it's different, it chose you.
Note that the people who made Apocalypse already had their minds set on a Phoenix retelling, since Days of Future Past erased X-Men 3's events, allowing them to. For instance, in an interview with CinemaBlend, Kinberg and Singer certainly had planted that seed, but it wasn't the full-on Phoenix yet.
As to whether Bryan Singer is interested in finally getting to execute his vision for the Phoenix, he was ambivalent to answer. "You never know, but as far as the idea of that brewing within her, I could, without giving anything away, say absolutely, you may find a piece of that in this film."