IMO it's all part of this push to combine mobile and desktop UI. On mobile there is a legitimate case to be made for removing them because screen real estate is so precious. But desktop gets clobbered as an unwanted side effect.
Notably, when you connect a traditional mouse, the scroll bar automatically becomes thicker (easier to click) and always visible, as mice users do have a reason to click/drag the scroll bar. Seems like Apple had this in mind
I've seen so many web pages whose "fold line" just aligned so neatly with the end of my viewport that without the scrollbar being visible I would've just closed the page, being disappointed that it's just a meaningless hero page with no content.
Similarly, if stuff like selection boxes align just right, you simply can't see there are more options without a scrollbar. It just looks like you only have those options that are on the screen right now.
It's just plain bad UX coming from Apple.
To me, it looks more related to the recent fashion of "minimal" interfaces. Like material design and ultra-skinny fonts. Could also be related to the "infinite scroll" some sites have. A scroll bar doesn't make much sense for those.
That said, the issues outlined in this article are glaring, and I do notice them when I switch to PC/Linux and a mouse and back. It's definitely something easy to forget, though.
The UX is designed to make most of the obviousness fade away and make the process an extension of your natural movements. Kind of like how a good band can take cues from each other without explicitly speaking or reading off of a sheet during a performance. But that doesn't help people who aren't adept professionals, or people operating under completely different circumstances.
I was adding another experience to the pile.