Doofenshmirtz rebuilt her with the intent to completely remove all of their killer robot programing for good because he didn't want to destroy them. He was able to sus out that they had gender dysphoria and is completely open to giving her a different body and Jane accepts. Doof spends 8-ish months rebuilding her to be more human like. They function more like an android.

They are genderflux, her gender identity is generally feminine. They don't identify as a Man™ but he's comfortable being a femboy sometimes. Sometimes she feels woman adjacent, sometimes she's genderless or has a very vauge sense of gender. Their presentation is always feminine leaning. They alternate between she/they and he/they.

'Cause you can't jump the track, we're like cars on a cable And life's like an hourglass glued to the table

No one can find the rewind button, boys So cradle your head in your hands

I headcannon that for awhile Perry was pretty creeped out by Norm for awhile. Especially after getting flung around like a yo-yo lol