“Something has gone seriously wrong,” dual-boot systems warn after Microsoft update

accidentally

Right.

How would they know if you're dual booting or not?

Windows, as any operating system, is best run in a context most useful to the user and appropriate for the user's technical level.

• Need to run Windows apps/games and aren't afraid to tinker around if and when something doesn't work as expected or your software simply isn't supported? WINE/Proton.
• Need to run mostly light Windows apps and don't want to tinker around? VM.
• Need to run Windows apps/games that don't rely on Kernel-Level Anti-Cheat, want direct hardware access and aren't afraid to tinker around, especially if you only have one GPU, and when something doesn't work as expected? KVM
• Need to run any Windows app/game without things constantly breaking or the need to tinker around and staying on top of things? Dual-Boot from different disks, utilize LUKS/FDE and be done with it.

Windows assuming it’s the only OS on the machine

That's not the case. The update was only meant to go out to Windows users. But Microsoft messed up and accidentally released to all users, or at least some who weren't supposed to receive it. My guess is that Microsoft usually doesn't update secure boot stuff for dual boot users and instead waits for the distro to push the update.