That just means that Samus was still in control. The transformation does start early, yes, but the behavioral effect of it doesn't start coming up until just before she fights the last E.M.M.I.
If she wasn't in control, she would have eaten the Raven Beak X. If she wasn't in control, a single word spoken by a computerized voice, which she's been associating with Raven Beak for the entire course of the adventure, wouldn't have stopped her. No text-to-speech "Yamero" is gonna stop her when she's really going
It is Quiet Robe, her family, who gives back her fullest control of herself; her conneciton to her kin is why her theme plays when she speaks to him, and why her only spoken words in the game are toward him, her family
And she isn't out of character if it's consistent with previous characterizations, but resulting in new behavior based on new stressors. That's in-character. She's just developing