If you have not done additional configuration, the automatic generation will determine the root filesystem of the system to boot for the configuration file.
For that to succeed it is important that the system is either booted or chrooted into.
By default the generation scripts automatically add menu entries for Arch Linux to any generated configuration.
See Multiboot USB drive#Boot entries and #Dual-booting for custom menu entries for other systems.
Usually you can do this by selecting the drive itself similar to how you would using BIOS.