Only the popover and app scrollbar can be interacted with. The original scrollbar for current note isn’t interactable without closing all popovers.
That said the darker outside scrollbar for the entire app is desirable. Basically what happens is if you open a popover that doesn’t fit within the obsidian app window then any portion of that note that doesn’t fit in the obsidian widow will be cut off. However, when that happens the obsidian app itself creates a scroll bar for the entire app (the black bar in your image)
So for example with my code a popover can be up to 800px tall. It will be smaller if the entirety of the note can fit in a smaller space. But if you have a really long note then the popover will be 800px tall.
But if you have your obsidian app window really small or you open a popover close to the bottom of the screen then you might only see the first 400px of the popover, the rest will be hidden below the obsidian app window. You can still scroll inside this popover to see most of it’s content but lets say you wanted to click something at the very bottom of the popover. Well you’ll be able to scroll to the bottom but that last 400px will still be cut off.
But since the obsidian app scrollbar exists what actually happens is first you scroll to the bottom of the popover and then when you hit the bottom if you try to scroll again then it will scroll the entire obsidian app down so that you can see the entire popover and reveal that hidden 400px.
moving your mouse outside the popover closes it tho so you can only do this via scrolling with the mouse wheel.
If your still confused make to really long notes and make them each have a page link to each other. Then continuously open an infinite number of popovers between them and see how it works.