The problem here is 100% that Apple, for some reason, provides both 16:10 "safe" resolutions and the actual whole screen resolutions. All those non-16:10 resolutions are a trap, because they cause the compositor to downscale the window to fit below the notch anyway -- they serve literally no point. There is no situation where a user would want a window that's 16:10.39 or whatever and then downscaled to fit within the bounds of the 16:10 safe area, so there is no reason to provide those 16:10.39 resolutions in the list of display modes.
Apple botched the implementation, but the hardware would've been perfectly reasonable and caused no issues or complexities for either users or developers if Apple hadn't botched the software.