TL;DR:
By the end of Apocalypse, Jean indeed seems in rather complete control of the powers she knows she has.
But had she known what she learned in Dark Phoenix, she might not have been.
The "Phoenix is Jean's alternate personality" thing is mostly irrelevant to that continuity, as
the Phoenix was portrayed more faithfully to the comics, with it being a cosmic entity. However Jean did have some "Phoenix traits", which is probably why it chose her.
By the end of Apocalypse, Jean indeed seems in rather complete control of her powers. Xavier knew that there was more to them, and she probably did as well, but never "set her mind" to unleash such firepower.
Why can Jean control these powers so well? It actually doesn't seem so unreasonable. Consider Jean's situation at that time: while some students aren't comfortable with her, she's overall loved. She has a home, people who care about her, some new friends with Kurt, and, obviously, Scott. Of course the whole Apocalypse doom is stressful, but mentally speaking, she's not in such a bad place.
Thus, she can be her true self and unleash enough/all power to take out Apocalypse. The "toning it back down" part seem more tricky, but once again, she's with friends now - even two of Apocalypse's Horsemen turned on him. There are no more foes, no one attacking her or threatening her friends. This power is hers to control, and it's "just" that, power. It's not an alternate personality, it's not a cosmic force, it's her power.
However, with the release of X-Men: Dark Phoenix, we come to learn that a good part of the above... May be wrong/a lie.
Jean indirectly caused the deaths of her parents, in a burst of power she couldn't control (she was ~8). After that, she was taken in by Charles Xavier, who taught her to control her powers, loved her, and told her she wasn't some broken thing to be fixed. Jean coped and moved on. But it's revealed that
Actually, Charles lied about her father. He survived the car crash, but thought Jean was a lost cause, considered his whole world to have died in the crash, and didn't come for her when Charles took her in.
Charles thought it better to hide that from her (she was an insecure 8-years-old), and possibly tamper with her mind as well.
Upon learning that, Jean reacted... Badly. True, the Phoenix Force within her didn't help, but even if that had not been here, she probably would have had a breakdown as well, once again, kid or no kid, we're talking about
A father rejecting his daughter.
So while Jean was shown in control at the end of Apocalypse, it has to be taken with a grain of salt, as an important consequence of her powers was hidden from her knowledge.
The Phoenix part is not technically covered by the question since the Phoenix is different from "her powers", but for the sake of completeness, Jean unsurprisingly underwent the "got a whole new power" workflow:
Can't control it, then seemingly can, then can't anymore, then can once and for all. She even appeared to have fused with it.
