Haven’t dual-booted in like 10 years, so I don’t have hands-on experience with it, but AFAIK that’s not really a problem since UEFI, or a much less common one.
Back then, with legacy BIOS computers, it booted by directly executing the first sector of the hard drive. This meant that there could only be one bootloader per disk, and so if Windows thought its bootloader was supposed to be used and it had an update, it just overwrote it. Or it would think it’s been corrupted/infected.
Now with UEFI, it’s its own partition and it supports having more than one there out of the box, so unless your boot process depends on detecting the default one rather than exactly which executable is the default, even if Windows updates it own as well as the default bootloader for a disk, it should be fine. Or at the very least it’s so much easier to just go to the firmware setup and change it back without having to reinstall LILO/syslinux/GRUB.