There's abundant evidence to suggest (practically confirmed desu) that Porygon-Z was designed for the Distortion World, and THAT'S why it behaves erratically. It is NOT glitchy, it just adapted to successfully suit the environment it was designed for. Things in the Distortion World are fucky, gravity is weird, waterfalls flow backward, things appear and disappear, etc. Team Galactic THOUGHT Porygon-Z was a buggy failure, but it wasn't. It adapted perfectly to fit its environment—which is why Porygon-Z has Adaptability but its family members do not. Why its head is now upside-down, and its body plan is abstract. Porygon-Z does not behave "abnormally", that's just what normal IS within the Distortion World.
If you're wanting hard evidence, look no further than in Platinum when an old man in Veilstone gifts you a Porygon and outright SAYS it "escaped from those Galactic goons". So Team Galactic had a Porygon, AND in Platinum you find the Dubious Disc inside the Galactic Veilstone HQ, AND Platinum is the first game to mention Porygon-Z was designed to explore alien dimensions. Team Galactic are CLEARLY the makers of the Dubious Disc, as if the name didn't already give that away. Porygon2's dex says it survives in the vacuum of space, but can't move in zero gravity. Well, the Distortion World says "fuck you" to gravity altogether, so Porygon-Z no longer has issues with this after being upgraded.
