The comics show the Phoenixes manifestation within Jean was purely to disinfect the planet:
https://imgur.com/rmWM4aQ
The comics show that Jean extracted Sublime from reality:
https://imgur.com/gmYWUFf
Following extracting Sublime, Jean states that the infection was so bad she decided to resort to amputating the future:
https://imgur.com/OKI2ENX
The Phoenix replies with "Phoenix disinfection successful" as regardless, Phoenix had accomplished her mission to remove Sublime from reality.
The Handbooks then clarify any ambiguity here telling us in the Here Comes Tomorrow profile that Jean disinfected reality specifically through the action of extracting Sublime:
https://imgur.com/NLy5H8C
The M'kraan crystal profile which would obviously have a different focus to the HCT profile addressed her statement that she chose to resort to amputating the future reality 15104:
https://imgur.com/hYE2YXA
As i said previously, neither handbook contradicts what's stated or depicted on panel or each other. They just focus on different things as ones a profile covering all the key narrative elements of the Here Comes Tomorrow reality, whilst the other is the profile of the multiversal M'kraan crystal, so the fact that a reality is severed from the multiverse, would be more relevant to said profile, than the in depth coverage of what happened in one of the many realities its associated with.
So both handbooks direct us on how to interpret said scenes and tell us what we should regard as canon. Jean extracted Sublime from reality thereby disinfecting it, she then decided to destroy this future by amputating it from the multiverse.
Jean is then stated on panel explicitly to have total telekinetic control of all of the atoms of the universe:
https://imgur.com/pfqD6pU
In response to this incident, the Handbook updated Jean's abilities.
Going from stating she had total telekinetic control of matter at the molecular level:
https://imgur.com/7gznS6V
to then updating and defining the scale at which she was canonically demonstrated to be able to use this power:
https://imgur.com/hYX4UPd
"allowing her to manipulate atomic structures on a universal scale."
So going forward, with the highlighted forum rulings on Handbooks being completely permissible as corroborating evidence, the feats above are to be treated as canon in forum debates. 👆