Over the last years, overlay scrollbars (which automatically hide when inactive) have become popular also in other projects (Unity, Mac OS X, recently GTK toolkit, probably more?) so I'd assume that designers considered advantages and disadvantages.
See e.g. the explanation for Unity and the followup.

I think this is also partially because nowadays users are not expected to click the scrollbar to scroll, since touchpads and mouses provide the means to scroll directly. In this sense, the scrollbar becomes more a visual cue than anything.

No, the scrollbar does not become a visual cue because it is no longer visible by default. You don't have any clue if there are thousand pages above the fold or one. When you write a comment, you don't see that there might be a preview below the submit button.

For my workflow, any time I have to wait for a program to do something means, well, I have to wait. If I have to wait and then aim for an invisible target because "the right of the fullscreen window" misses it (cf. T89842), I'd probably have more fun playing Flappy Bird. Any time I have to learn or remember a different UI just because it is a different application is time lost.

Phabricator is a tool for me to do work. It's stated goal is productivity. I don't care when overlay scrollbars impede my workflow, as long as the overall productivity increases. I haven't seen any evidence that it does.

It might be interesting to know in which situations it matters to know where exactly you are on a page (and how often these situations happen). My workflow and/or hardware might be different so I'd like to understand. Personally I use the "Home" and "End" buttons of my physical keyboard if I want to go either to the top information or to the bottom comment box; and apart from that I basically only scroll down when reading comments.

Isn't this task a duplicate of T89842: Don't override OS scrollbars on Phabricator ?