You don't play as Samus in Other M.
You play as her clone.
The entire thing is out of character for Samus. It all happens on a research station where the Federation is cloning everything. The bad guy is a human clone that looks more like Samus than the doctor that allegedly supplied the DNA.
Her suit's Chozo tech, not federation, why would she let them place remote locks on all the functions?
The only explanation that makes any sense is that the Federation cloned Samus as well and gave her info that they scanned from her after the events of super metroid, then tried to regress her back to a mental state where she'd be willing to listen to her old CO(who might also be a clone).
All of this makes sense and kind of HAS to be true.
In the opening of Fusion, she states that her dealing with her new ADAM computer is the second time she's had to take orders.
So in canon she has stated that she never experienced the events of Other M.
So that part's pretty provable, but the next part's speculation...
Samus would surely know if there was another one of her running around hunting bounties, wouldn't she?
The Federation knows that, and didn't want her to just Samus it up. They want an extra Samus on hand in case they need her and the original won't take on a mission for them. So most of her time has to be spent in cryogenic freezing, probably on a space station specializing in biological research with Space Federation ties, right...?
The federation says that after they cut off most of her suit (literally just the parts with all her suit abilities, mind you) the X parasite just sort of grew a new Samus inside of itself.
But the main plot of Fusion is that the Federation lies. All the time. I think the X parasite took over everything on the station, including a frozen Samus clone, and that's what became the SA-X.
In Fusion, Samus describes SA-X as like her, but without her humanity. That sounds like people's issues with Samus in Other M.