Magneto's shield would always be up in a situation like this, and his shield can stand up to hits from the likes of Marvel's Hercules (who is a tier higher than the characters in this slot, for persepctive), Thor, the Hulk, and even incredibly powerful foes that absolutely dwarf both himself and especially Medamatcha like the Phoenix and Galactus have had a hard time or at least some difficulty overcoming his shield. Obviously, in a 1-on-1 fight against beings that powerful Magneto wouldn't stand much of a chance, but the point is that his shield is so powerful that Medamatcha and his little gremlins aren't going to be able to get through it.
As far as speed goes, while DB has very flash feats of speed that make it seem out of Magneto's reach, I don't actually think he's outclassed here at all. He regularly reacts to opponents like Quicksilver, Thor (who regularly travels and fights with FTL opponents), and the aforementioned cosmic forces. More objectively, here he is manipulating two lasers after they have already started firing. Lasers, as we know, travel at the speed of light, so that's him reacting to two distinct sources of FTL threats coming right at him and deflecting them both seamlessly.
An important advantage for Magneto is that he's actually smart. We never see any evidence that Medamatcha is even capable of advanced thought really. Magneto, on the other hand, regularly orchestrates schemes and battle strategies against the likes of Professor X and other incredibly intelligent Marvel geniuses, both in combat scenarios and in more general "world conquering" scenarios as well. Medamatcha, on the other hand, only really has one method of attacking, he is restricted to melee combat almost exclusively as far as I remember, and he doesn't have any good feats of endurance or longevity on the battlefield. You say Medamatcha will outlast Magneto, but I think the opposite is much more likely. Pre-Namek Saga Goku simply powering up was enough to kill him, and that same Goku is also in this power tier, so I honestly sort of don't think he even belongs in this power tier.
Also, any lifeform we know of has metal in its blood. To argue that Medamatcha doesn't would require some form of evidence in my eyes. Magneto has experience with aliens, and can detect metal naturally. That's just an aspect of his power. There's every chance that he can just rip the metal out of Medamatcha and get an easy win, as Medamatcha has no feats of endurance that would survive that, nor any power than suggests he could resist it.
But let's assume he doesn't have metal in his blood. Again, there's no real reason to do that, but let's assume for the sake of argument. Magneto has such a wide variety of powers that he doesn't need his opponent to have metal in their blood to beat them, nor does he need a direct source of metal. Here he is BFR-ing Hercules (again, a tier above these fighters) with nothing but rocks. He can deactivate brains with an EMP (somehow). He can shoot energy lasers, which are strong enough to go through this Holocaust guy's armor and seemingly break mountains. He can also sometimes just do things like this. Medamatcha doesn't seem to have any defense against Magneto just using electromagnetic forces to tear him apart like that. I assume that's what's happening here anyway.
In short, Magneto's shield is basically going to be impenetrable here, He is a much smarter fighter, he has a much bigger variety of powers, and he regularly stacks up to opponents who are far stronger than Medamatcha, like Hercules and Thor. There's also no reason to assume that Medamatcha is immune to just getting the metal in his blood ripped out. Magneto should comfortably take this