I hope that there simply hasn't been enough work done to do a category-theoretic treatment of all of these topics, and that perhaps even more category theory itself needs to be developed so that there are good ways to talk about concepts that are almost-but-not-quite-entirely described or subsumed by category theory.
The alternative is that I'm painfully wrong about what applied category theory aims to be, and that I have a ton of application-specific terms to learn about and won't find a formalization of the sense in which all of these concepts relate.
[1] https://en.wikibooks.org/wiki/Understanding_Darcs/Patch_theo...
[2] https://github.com/trailofbits/graphtage
[3] http://bx-community.wikidot.com
[4] https://github.com/grammarware/bx-parsing
[5] https://en.wikipedia.org/wiki/QVT
[6] http://graphdatamodeling.com/Graph%20Data%20Modeling/GraphQL...
[7] https://neo4j.com/developer/guide-data-modeling/
[8] https://web-cats.gitlab.io/#some-of-the-cats-we-come-across
[9] http://pauillac.inria.fr/~pilkiewi/papers/boomerang-tr.pdf