I suspect this is a case of confusing epistemology with ontology.
Galaxies are ontologically composite in that they're the highest holonym in the supervenience hierarchy [0]. Atoms are ontologically fundamental in that they're the the lowest meronym in the supervenience heirarchy.
Galaxies are epistemically abstract in that the notion of galaxy is far removed from everyday experience. Atoms are also epistemically abstract in that the notion of atoms are also far removed from everyday experience. What's epistemically fundamental are the immediate objects of our everyday experience, like chairs and food. (My impression of Zen is that it advises to focus more on things like chairs and food [1].)
In the xkcd, which is more "fundamental", Math or Economics? Well, it depends. Likewise, what's more "fundamental", bits or ADT's? Well, it depends.
[0] powers of 10: https://www.youtube.com/watch?v=0fKBhvDjuy0
[1] http://www.itsokblog.com/2011/01/wash-your-bowl-zen-of-mothe...