I don't really see why Magnezone lv. x would be such a huge threat. If it's hit with a status effect it can't use Electric Trans, and if it retreats for free with the regular form's Body to get rid of status afflictions to enable Electric Trans, it is going to have to rely on Warp or Switch to get it back out there to attack that turn. Special Metal energy wouldn't seem to matter much with poison/burn in the mix, enabling it to be 2HKOed enough of the time. I'd also say Scorpio would have the speed advantage. Finally, Gliscor lv. X's ability to do essentially what Magnezone lv. X does (auto-paralyze followed by 80) would seem to further equalize things if not swing them in Scorpio's favor. If I was playing against this deck I would likely hold off on even playing Gliscor lv. X until they had already leveled up Magnezone, so that when it was paralyzed they'd have no way out of that aside from Switch/Warp Point.
The only way I can really see things slipping for Scorpio is if the opponent managed to get 2 Magnezone lv. X in play (as well as Electivire of course), because then they could retreat 2 tanks freely while retrieving and swapping energy and there would be no way to shut down Electric Trans. However, going back to the speed advantage Scorpio should have, I don't think it would be so easy for the Magnezone player to get that well set up to begin with. The reusability of Gliscor lv. X would also come in handy if that deck DID get so well set up. It'd consistently be getting a taste of its own medicine.