The only thing that possibly CAN make sense, given the continued existence and floating of Pony Head and several other obviously-magical creatures is that "The Magic" is not the same as "all magic."
"The Magic" is presumably a specific font and source of power overseen by Glossaryck and Glossaryck accessories like that one female Glossaryck from that Ludo episode
. This is the font of power that the Butterfly lineage has drawn from, and that the Magic High Commission oversaw, but it's unclear what else it is and is not responsible for. For example, Septarian regeneration doesn't appear to draw from The Magic, as Toffee was pretty strongly opposed to The Magic, but their regeneration is too rapid and extensive to be without supernatural elements. Similarly, nobody ever talked about Globgor as a magic-user, and yet he's capable of changing size in some kind of way.
If "The Magic" is simply one power source, it's possible that most of the Star Vs. multiverse is unaffected by this change. While Hekapoo may be out of commission--we don't know for sure, as she was the only member of the MHC to not show some kind of corpse--it's entirely possible that other supernatural methods of creating dimensional portals could exist.