An Addendum
Further rewatches and pondering over Z's three episodes has led to an intriguing discovery. Z's relationship with Baxter definitely changes from season 3 to season 7, but not only in the ways people generally remember.
In Bye, Bye, Fly, they've just met. Z is sociable, inquisitive, and friendly, and he wants a friend. He sets about trying to be a friend, even though he doesn't know how. He's also a little more formal/computer-like and Baxter doesn't always like Z telling him ideas on what to do. He betrays Baxter while being tortured, but doesn't expressly try to rectify it.
In Son of Return of the Fly II, Baxter's mind is going and Z assumes a more leadership role and tries to soothe and comfort Baxter and reassure him that he'll help him. He seems to get plans of his own after gaining a body, but he never forgets Baxter in those plans. He is cheerful and playful at times, moreso than in season 3, and no longer treats Baxter in a semi-formal manner.
Revenge of the Fly is where the differences are both most striking and most sad. Z is darker than in season 3 or 4. He is no longer cheerful and doesn't smile as widely as he used to, although he takes a dark amusement in the chaos. He is more subdued, yet also absolutely fiercely protective of Baxter. He proclaims Baxter his best friend, something he hasn't said before in spite of all the pet names, and turns the Technodrome upsidedown for him. Again he betrays Baxter to some extent when threatened, but this time he does try to repair it as soon as he has an opening. He also snarls at the Turtles that Baxter will get them. Instead of having any separate goals of his own, now he seems to live only for Baxter.
Baxter and Z are all each other has and it's logical that they cling to each other for companionship. But while Baxter's mind is collapsing from the fly's takeover and he is becoming more and more like a child, Z is growing darker and more vicious. It could be the strain of watching his only friend crumble into madness. Perhaps also, a growing bitterness over all the pain Baxter is going through. And maybe too, a deep love that has blossomed and is manifesting as a furious determination and desperation to see no further harm come to him. Z longed for a friend, but he didn't realize how having someone to care for would change him. He may not even realize himself how much he's changed, but he is clearly different from season 3 or even 4 by season 7. It's a quiet progression, and may not have even been intended by David Wise, but it's there.