Yeah, I don't see Shadow DOM often, but there are couple sites I use that employ it - most notably Gerrit. Since I use it almost every work day, I wanted to fix a bunch of UX annoyances it has. Those fixes would've normally been trivial, but Gerrit UI has everything wrapped in multiple levels of Shadow DOM, making those fixes near-impossible instead to do in Stylus alone.
Some combination of Tampermonkey, MutationObserver and IntersectionObserver almost always gets there in the end, but despite having a default user script template with this exact skeleton it's a lot more of a pain in the arse to achieve what a simple CSS selector and some properties does in a few lines...
Exactly. And for me, that difference in PITA is the difference between fixing up websites in Stylus incrementally, spending a couple minutes for a CSS rule or three when something annoys me, vs. making a note on my TODO list to write the necessary code later, and never getting around to doing it.