GLADLY :)

While Dr. Julien was building Zane, he made him have the same traits as a regular human(consuming, feeling, all that). Zane was made to be gentle and a son. After Dr. Julien erased his memory, Zane spent all his life thinking they were human, and the other ninja also thought he was human as well, plus they were all implied to be teenagers in the pilots-s2. In retrospect, it could be that he was average height.

In Pixal's case however, she's visibly an android. She probably didn't have the same traits Zane had when she was first built. Pixal was made to assist Cyrus Borg, who is handicapped, therefore, probably not able to reach up high. In my own personal opinion, what's the point of building a robot that's made to assist you if they aren't tall? Ik you could kinda use this argument with Zane, but as I stated before, he was made to be gentle and a son. And the interior in Borg's office(I think that's the room) is HUGE, don't tell me that Cyrus doesn't have trouble getting those materials, yes you could bring up the spider thing he had in the beginning of s3 but I don't think it could really go up that high. Pixal was an android made to assist humans. It makes more sense that she's the one taller throughout season 3.

Alright, pilots and s3 out of the way. Time for when both of them rebuilt themselves :3

Zane rebuilding himself to be taller than Pixal after his death does make sense in some sort of way. But after Pixal got scrapped, she rebuilt herself to save her father in s7. She rebuilt herself so she could fight and quite literally defeated the embodiment of death single handedly. Pixal had to rebuilt her body so she could fit the Samurai X suit, but later on, she comes back with a completely new one, and do not tell me that her suit doesn't add a few couple 2-3 inches to her height. Her Samurai X suit intimated the villains back in s8 so there's some points there, but i still fully believe she rebuilt her body without the suit to look gentle, and she is. Zane still had that gentle look and 100% built some deadly weapons in him.

Now I am not done.

Zane obviously has a habit of throwing himself into danger to protect his loved ones. Pixal has seen this time and time again while being in his head and witnessing his death in s3. Watching your partner injured or becoming close to death and not being able to do anything is GOING to do something to you. It makes sense that she would want to protect him. Hence, building herself to be taller so she could.

Zane's most likely never going to let go of that habit even if you would punch it into his head. Pixal 100% knows this you can't say otherwise.

Thank you for very kindly asking😁

@graceful-not