Changing the appearance and the behavior of scrollbars (or replacing them entirely as you mention) are very different concerns.
Not really, it's the same concern; the potential for gratuitous, superfluous, or regressive modification of a stable and predictable user interface element that is representative of the most fundamental of actions when it comes to long-form document-based design: scrolling.
A browser-wide scrollbar styling system, able to be opted into by use of particular CSS, doesn’t imply anything about whether we are talking about just one scroll bar or all of them.
I also disagree about native controls not always being the best solution when it comes to scrolling. We all know how annoying it is when a page jacks scrolling; it’s a usability nightmare that makes pages’ scroll behaviour harder to predict. We don’t need to add to the usability issues by letting one of the most fundamental pieces of chrome in a web browser get jacked even further than the already impermissible state.