the boot manager I use to dual boot them (the Linux BURG) needed no change whatsoever and booted the newly-AHCI disk without ever batting an eye...
Bootloaders typically use the boot firmware (UEFI/BIOS) to access the disk. Its the OS kernel that does its own thing.
Windows is no different here either, just that it acts like a retard when things change. Linux and BSD just take it in their stride.