True, but in this universe, what Equestrian magic does (creating energy or matter essentially out of nothing) would violate basic laws of physics like the conservation of matter and energy. Discord, in particular, seems to be able to create pretty much anything at will. The fundamental laws of nature differ in other ways, too, such as, for instance, that there is no such thing as "raising the sun and moon" in our universe, because we actually orbit them. In Equestria, these are objects that can be controlled.
Similarly, the weather control abilities of pegasi shouldn't work here. Even earth ponies, by their mere presence, cause plants to grow faster.
So if Equestrian magic worked here, it would have to be able to violate the laws of physics in this universe.
Conversely, laws like the conservation of matter and energy are exactly why something like a nuclear bomb works. The process of fission essentially converts a small amount of matter (or specifically the binding energy holding together nuclei) into energy. If there's no mass-energy equivalence, there's no reason for that to work in Equestria.
Some things seem to work the same, or at least on the surface. There seems to be flame and candles work, for instance. But perhaps they work on phlogiston or something that doesn't exist here.
(My post reminds me of the MST3K theme song, the part that goes
If you're wondering how he eats and breathes.
And other science facts,
Just repeat to yourself "It's just a show,
I should really just relax."
But I find it fun to try to justify these things.)