ironic that the benefit of using web tech (platform abstractions) can be totally negated by such a small footgun, which then requires insane knowledge of the browser rendering pipeline to solve
If you expect to make a note taking app, which only has a piece of text, a stop button and a floating animation, I hope that you figure out why your performance is being tanked by your single animation.
Saying it having not much of that knowledge myself: it's reasonable to sometimes need platform knowledge to make intricate things (here a realtime animation) behave efficiently.
That's the same for game engines, native rendering, flash animations etc. There will always be edge cases, building enough stuff you'll hit them, and if you care about doing it right it will require knowledge to overcome the issues.