How does running water ground out a wizard's power?
How does digesting tin sharpen one's senses?
What's an Epstein drive?
Why does a binary star's jump points come and go when systems with single stars have stable ones?
Whether the science (or magic) is nonsense or not doesn't really matter. What' matters is that the nonsense gets applied in a consistent manner. You make it predictable by giving them rules: "You can get x y and z effects by running electric currents through magic rocks. But not a b or c" Reality doesn't define the rules in fiction: the rules define the reality.
It absolutely matters whether it's nonsense. Because you can't make nonsense predictable. That's the whole point. If it was predictable and governed by clear rules, it's not nonsense. It's coherent abstract theory. It's an actual cosmological philosophy, or actual theoretical physics.
When you start with an idea that, fundamentally, is nonsensical, and you desperately try to shoehorn that idea into a system of semi-coherent rules that don't necessarily hang together and are designed to be tested externally by empirical reality (science) what you get is gibberish.
I don't understand how this point is controversial. How can you think nonsense has predictable, logical rules? If it had predictable, logical rules, it wouldn't be nonsense. In fact, if you could create a - fake - internally consistent theory of space travel that allowed FTL, you'd be revered as one of the greatest living intellectuals and philosophers in human history. It's not clear anyone has ever created this theory, even purely theoretically.
Let's say we get Neil deGrasse Tyson here. We tell him: we have magic space rocks that allow for FTL travel and gravity manipulation by a complete unknown mechanism. Now invent an internally consistent theory unifying all of physics with this abstract thesis to allow space travel. He'd have to come up with a Grand Unified Theory of physics all on his own, starting from a postulate that doesn't make sense.
Writers can struggle to come up with generally plausible sounding rules that most of the time are applied in a kind of reasonable way. But they can't do more than this tiny thing. IRL, we can't even do this with the law, which is an entire system designed by its fundamental nature to be a logically consistent and internally coherent set of rules, designed exclusively by people and absolutely not tested against empirical reality. The idea we can create internally consistent rules is nonsense, and wrong.