CSS animations are a pain-inducing non-starter for thousands of recurring use cases.
Example: Using Javascript to SHOW a modal, but then relying applying addClass('animate') using CSS animations to transition that modal (eg: bottom of screen to center, while fading in) are nearly impossible without tons of hackery. The animations do not render.
Hence jQuery animation calls.
What you’ve described is actually pretty simple to do with CSS Animations. Just not with CSS Transitions, which is what people usually use.
CSS animations are a necessity if you want any kind of performance on mobile browsers and older phones.
The final thing I used to reach for jQuery for was animation support, but that need is by and large gone now. AJAX/JSONP is good there, but to be honest it's not something that needs a wrapper these days.
Glad to see the library is still updated, though - for sites that might not have a budget to upgrade, knowing it's still got support must be nice.