Magne-evolutions are pretty much unbeatable in Factory Field arenas, they get both their STAB moves significantly boosted in the Field, regardless of whether or not it is activated. Factory Fields also happen to pop up most often in the game, especially when you're fighting Team meteor. Not to mention many of those are double battles where your Discharge can hit both opponents. Taking all of that into account, and the fact that you can currently catch Magnemite in the ONLY Gym that uses the factory field and subsequently shit on Shade's day using that very Magnemite, it only makes sense that they would bump him up to a much later catch.
Uh, considering you can't get Mega Ampharos till pretty much the end of Episode 17, i'm assuming you mean regular Ampharos. In which case, the list of "next closest" is kinda damn long.
Vikavolt, Eelektross, Alolan Golem, Rotom-W, Jolteon and Galvantula are all pokemon you should CERTAINLY consider over damn Ampharos at any given situation. In fact, some of these pokemon may prove more valuable than Magnezone under differing circumstances.
Jolteon is fast as heck and you can get it much earlier than Magnezone, meaning it easily compensates for the meager 5 base SpA Magneton has on it. Eelektross, for all intents and purposes has no weaknesses, is versatile as heck and provides your team with a painfully important ground immunity. Rotom-W kinda does the same things but better. Alolan Golem packs some of the most powerful hits in the entire game. And Galvantula is the premier sticky web setter, up there with Araquanid. So there is no way in hell Magnemite is getting gibbed JUST because it's a good electric type.