When the top right corner contains a search field instead of rounded button, that also seems to use varying curvature instead of capsule with proper circles at the ends. Still results in varying spacing between window corner and the toolbar content.
And that's just the 2 top corners. Attempts to align top corners result in even bigger mismatch with the rest of the window content. For example calculator -> it has a grid of round buttons. While the window corners might match top bar (as good as they can due to different shapes) the main calculation buttons don't match the corners at all.
Similar problem affects many of the popups which have something like confirmation button anchored to bottom right corner.
Rounded scrollbar handle - not aligned with bottom left corner size, instead it awkwardly gets cut of by different amount in each program.
Menus also have this disease. The non circular corner curve of overall menu shape extends way past the corner of item highlight resulting in varying spacing and making it feel almost like whole menu has bulged out instead of flat sides.