No, I didn't miss the point at all.You’ve missed his point completely. It wasn’t about science fiction technology vs magic at all. And it wasn’t about magic dilithium crystals vs magic time crystals either.
The point was that there’s this incredible new technology that only Mudd has, the time crystals, technology that allows you to repeat a specific period of time in a specific spot in the universe an infinite number of times, technology as groundbreaking as the spore drive, technology more groundbreaking than the invisibility cloak, technology that’s invaluable to the war effort for both sides, and nobody cares? WTF? Screw the mushroom drive, Mudd should have sold this to the Klingons!
If the time crystals were going to be a regular thing, tI'd agree that they are too powerful and ruin the story. So, the complaint would be that they're story elements that ruin the drama and NOT that they're "magic crystals." That's why the magic crystal thing just doesn't hold water.
Fortunately, it appears they were just introduced as a means to tell this particular story, which is fine. So, these were just super rare crystals won't appear again. That's fine.