Controls that only reveal on hover are extremely user-aggressive, especially when part of their job is to indicate the current status of a view ('can I scroll any further?'). UIs should keep user informed, not hide information because it "looks prettier."
Always-visible arrows have a large set of usability benefits:
the user always knows where they are on screen and can move their pointer to interact with them without having to first move to the scrollbar, then to the arrows, or memorise the positioning of the arrows.
they always perform their job of indicating whether or not the user is at the end of a scroll view.
That point is especially important because the current status quo means that a user can't quickly tell if a scrollbar is at the end of its track without hovering over it, due to the gap created by invisible arrows.
Users enabling scrollbar arrows are also likely to prefer a more utilitarian than a more 'sleek' UI, so this caters to them better.