But yeah, using the uefi works fine to choose between windows and linux, even if you only have a single /efi partition (I use efistub for linux, not a dedicated bootloader).
If you add custom boot options, they won't be removed after a windows install, it only adds itself to the list and sets itself as the first in line. Afterwards, it doesn't seem to touch that anymore, but YMMV with "big" updates.
I had OSes on separate disks. Win7 and Arch, used UEFI to choose who to boot.
Updated to Win10 and it somehow completely broke Linux boot. I could choose on UEFI to boot Linux but it wouldn't work. Eventually I gave up and reinstalled Linux
In UEFI? If I have the OSes on separate physical disks I'm planning to use the bios to select what boots.