Except for a few of his abilities such as accelerated regenerative healing, shielding others from telepaths, detecting a telepath in his own head, and teleporting, Apocalypse's pupils and irises have been consistently seen going white while using any of his other abilities in the movie. If you look at the scenes wherein he makes Storm, Angel, and Psylocke reach their full potentials closely, you'd see that his eyes going white matches the exact duration of their transformations, no more, no less. I'd also like to stress that Apocalypse isn't just giving them new/additional abilities, he's just manifesting the full potential of their respective X-genes, which the individuals in question might've unlocked eventually over time by constantly pushing themselves, they might've not. This version of Apocalypse doesn't have the ability to give others powers, unlike the comic book's Earth-616 version who can do exactly that using the technology of the Celestials that he happens to own. So he did not give Angel metallic wings per se, he just unlocked the full potential of the X-gene that Angel had which resulted in a secondary mutation of metallic wings also getting expressed. I'd also like to point out that he hasn't necessarily made them Omega level mutants either. For a mutant to be an Omega level mutant:
- The X-gene that they happen to have should provide them with an ability which theoretically has the capacity to be an Omega level ability if exhibited at an extreme level. So if a mutant just has the ability to make their body parts go blue, the most extreme version of that ability would be to make their entire body blue, this ability, even at its most extreme capacity, wouldn't qualify as Omega level.
- The X-gene itself should have the propensity for the Omega level expression of itself native to it. Even though the example in the previous point already fails to qualify as an Omega level ability, assume, for this point, that it does. So the X-gene would have to have the potential of making the mutant's body go entirely blue if the mutant is to go Omega level at any point in the future, if the X-gene only provides the ability to make your hands turn blue and maxes out at that, if that's the expression of the X-gene to its full potential, you can't become an Omega level mutant.
- The potential being talked about in the point above needs to be expressed fully. The movie version of Apocalypse can obviously only do this.
While it's true that he did use his powers to unlock the full potentials of Storm, Psylocke, and Angel, one can also notice that his eyes never go white while Magneto uncovers the full extent of his own abilities. All Magneto gets from Apocalypse is the villain's version of a pep talk. Magneto had an X-gene with the propensity for an Omega level ability since day one which had genotypically expressed itself to its full potential, it was just a matter of motivation for him to exhibit the exact extent of his phenotype, of his ability, of his powers. This makes the question of Magneto "retaining" that extent of his powers moot altogether. Moreover, we know for a fact that Storm also retained her abilities cause before the helping hand from Apocalypse, all she could do is make minor gales, but after that she displayed weather manipulation techniques that allowed her to conjure up bolts of lightning intense enough to render Apocalypse unable to teleport. This degree of weather manipulation is consistent with the kind of weather manipulation we've seen from Storm in the original trilogy. Even if Apocalypse never woke up in the original timeline and the new timeline which coalesced due to the Days of Future Past is where Apocalypse awakens, that still doesn't change the fact that Logan wakes up in a future which is identical to the original trilogy's timeline (with the exception of The Last Stand) at the end of Days of Future Past; complete with Halle Berry's Storm with her same grey-white hair look. We have no reason to believe that everything was like the original timeline at the end of Days of Future Past but Storm's abilities weren't.
Coming to Charles now, Charles's full potential wasn't unlocked by Apocalypse. Apocalypse just replaced Cerebro in that process, that's it. Why else would Apocalypse's eyes going white only last until the relaying of the message, why was there no discrepancy in their respective durations? Besides, if he wanted to permanently amp Charles, would it not make sense for him to get it done and dusted beforehand instead of doing it at the same time as he's having Charles relay the message? Moreover, it is also known that Apocalypse usually only has 4 horsemen at once, something that the movie explicitly foreshadowed as well. He already had his 4 horsemen by his side at that point, none of them had defected yet and they hadn't even disappointed him in any other way. He only unlocks the potential of his prospective co-conspirators that he'd recruit as his horesemen thereafter. Besides, Apocalypse also wanted to transfer his own consciousness to Charles's body, so it wouldn't make sense for him to unlock Charles's full potential beforehand when he can make Charles's body go through it once his consciousness resides within it. Not to mention that making Charles that powerful before the transference would just lend itself to further hindrances in him transferring his consciousness into Charles's body, something that Apocalypse would've obviously considered.