I have to ask. Why do people dislike this? The browser scroll bar is often ugly as sin. Also its useful when having more than one area that needs scrolling capability without having that ugly default scrollbar junk up the middle of the screen in said application.
Look at the name people give it. Scroll-hijacking. The web designer hijacked the scroll action and modified the behavior to something other than the os and/or browser level setting. When I scroll, I expect to scroll based on the settings in my browser. I don't want your website to stop scrolling and use my scroll action to play through the frames of your slow-loading animation. I just want to scroll down and keep reading.
It's not the appearance so much as the behavior. For example, I have (probably like many) an intimate muscle memory associated with the sensitivity of my touch pad for scrolling. The deviation from how I expect the software to behave using the same physical interactions I normally use suddenly makes me feel like a clumsy oaf.
I have a touchscreen laptop, so the inertial scrolling often gets broken when sites scrolljack. That said, styling the default scrollbar (except in Firefox, where it can't be done) is a different behaviour, and whilst imho it should be discouraged for "regular" sites like this example, is totally fine when scrolling small widgets.
There are some (very few, rare) scroll-hijackers that work pretty well. This one is not one of them. In fact, the one used on this site is one of the worst. Why I say this is its behavior. Instead of smooth scrolls, it seems like there is a certain threshold at which the scroll bar "ticks." They mask this tick by slapping on it a tween animation. So it's a bunch of ticks that result in tween animations. There are beautiful scroll-hijackers that use complicated math to make it an actually smooth experience. This one is neither smooth nor helpful. There are also those scroll-hijackers that are employed to do card/slide/page based interfaces. Those are still awful, much more understandable than this garbage.
I hate it because it completely distorts my view of how the input works. It's just as annoying as changing the velocity of the mouse on a page. Don't mess with inputs.