I am running Antergos Linux (64-bit) with Gnome version 3.22.2 at 4K resolution.
I have Tweaks -> Windows -> HiDPI -> Window Scaling is set to 2 and my mouse cursor size is set to 48 (gsettings set org.gnome.desktop.interface cursor-size 48).

I noticed that both window scaling and mouse cursor size are applied too late during gnome-shell loading process, that causes some extensions to set their sizes in regular, not scaled, pixels. For example, one of the extensions I use, called dash-to-panel, was not setting its size correctly during startup, but was doing it correctly after restarting gnome-shell by typing 'r' in the "Enter a Command" dialog due to this issue. The author of the extension created a workaround for this issue by listening to the scaling change event and refreshing the panel. You can find the issue discussed here https://github.com/jderose9/dash-to-panel/issues/57

The other issue is also related to scaling, but of a mouse cursor. Even with ALL extensions disabled I can clearly see that my mouse cursor is tiny (24px at 4K) when I hover over the top panel just after gnome-shell has finished loading. The problem disappears after moving my mouse cursor around the screen for some time and hovering it over the top panel again.

I don't have deep understanding of how the scaling works, but I think the problem is in timing, the setting should be applied before anything is drawn on screen.