I believe he rationalized it as his being "triggered" by her "transfobia" and lashing out.
It's total birdshit, of coure. Phil constantly flip-flopping his mother' stance on LGBT within his narrative. When he visited her and she bought him pizza she was apparently totally cool with him! Then months later he cursed her (and her bf, and his dad, etc...) out for being a bigot.
I'd like to remind to everyone that prior to his battery of the poor woman Phil stole his childhood photo albums from his mother's closet and burnt them all. He triumphly posted the evidence on deviantArt, claiming it was for her own good, so that she'd better accepting her "daughter". Even being such a hugbox as it is, it was easy for dA to realize that his true intention was to hurt his mother, a retaliation for their prior argument, and they called him out on it. Fuck Phil.