If you use OBS, a game capture works the same way, it hooks the DirectX (or whatever API) functions to grab the rendered scene directly. It often has issues picking up overlays because there isn't really any synchronisation, just whatever made the last detour fires first. Like the sibling commit says, you can stack detours, it's only an issue for OBS if something that runs after it renders more things to the screen.

There is a setting to make it pick up overlays, which works reasonably well, I'm not entirely sure how it's implemented.