Dumb title. Yes, it's safe. Windows has nerfed boot records for any other OS since the beginning of dual-booting. Just replace the boot record.
Also, if you want to be hardcore about it, and since everything is UEFI now, just use your BIOS boot manager to control booting. Shouldn't be a problem.
It doesn't change the preferences but it does replace bootx64.efi which is the default bootloader executable for a drive, when the UEFI doesn't have more specific entries. In some configurations both Windows and GRUB want to be that.
If you add a boot entry for GRUB and don't point it to the default executable, then it won't be affected. Until you reset the BIOS or try to use the drive in another system that is, in which case the firmware will then only know about the default executable. But it's easy to add the boot entries back.