What I'm describing is exactly the situation now. Many people dual boot Windows & Linux, with kernel level anti-cheat on their Windows partition. The existence of Linux on the same computer does not prevent the kernel level anti-cheat from working on Windows.
Similarly, the presence of unsigned software on a computer would not stop a Linux kernel level anti-cheat from working, and the kernel level anti-cheat shouldn't prevent the unsigned software from working. Once you run that unsigned software, your machine is tainted similarly to the way your kernel is tainted if you load the NVidia driver.