tl;dr you'd have to be a bit insane and obsessive to do these things, but it very likely CAN be done.
I thought about this as well, though I have zero complaints about the magnet strength being too weak. I run with yellows. I'd just like more variety, because I'm a nerd.
Examining them, they look like they have a tighter precision than usual plastic manufacturing, and they're pretty hard. Looks like they did a good job on them, no burrs or anything. (good, because it's not a cheap cube, and it would mess up the concept). Plus they have those ridges to lock them in.
the closest I came to was somebody could map for a 3D printer, and then somebody with a very accurate machine could make batches of the capsules. The magnet enclosure would be open, so magnets of proper size could be pushed in (but I doubt they could be removed without messing up the plastic. it would be one-shot installs, otherwise the magnets would become loose. the plastic would have to be slightly smaller than the magnet size, or have some kind of locking mechanism)
it would be ideal tbh if GAN would release empty capsules so magnets of choice could be put in, but then polarity would become an issue if not done right, and also inconsistent strengths from cheap magnets (GAN totally did it right with the X omg, it's pricey for good reason. I've tried many magnet combinations, and you can definitely tell if you have even one different capsule installed.)
for an example of how it could go wrong (sorry this happened, Cube Solve Hero! Thanks for the PSA T_T )
as far as modding the empty capsules, if you look closely, you can see the enclosure is pretty exposed, as well as the sides. they saved on weight by removing unnecessary plastic all around it. Impressive design, GAN!
you could probably sand down the tops with a very fine grit until you expose the hollow point, push in a magnet, then test. if the magnet is loose, you could put a microdrop of superglue into the hollow, then put the magnet in. be careful to not round off the edges, it would have to be very flat. Given this, you could probably mod the other capsules as well, if you could coax the magnets out without much damage. you'd need machinery
I doubt it would be worth all this effort, and you'd certainly mess at least one up.
another alternative is to break open the cubies and glue them old school

or drill into another cube then glue magnets into the holes haha (those aren't serious suggestions

)