That's true, though I'm increasingly wondering whether that's a bad thing. Emacs can be run in "batch mode", so it could be used just like every other stage in the pipeline (a bit heavy, though not much compared to modern tools). Then again, I never tried it.
When I started writing a static site generator powering my current personal site, I wanted to parse .org files in the generator. I very quickly gave up and decided to manually export my .org posts to HTML, and parse that instead (see [0]). I didn't realize back then that Pandoc can handle .org files; I probably would have decided to shell out to it instead. Then again, if there's one thing I learned writing a static site generator (twice), it's that the next time around, I'll pick up one that's already written by someone else :).
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[0] - https://news.ycombinator.com/item?id=19622751