In my BIOS settings, I can go into config > boot > boot order. From there, I can tell it to check the USB first, followed by the hard drive, then the CD, network, etc. etc. even if those devices are not actively present. Do you have such an equivalent option, or does it only show “present” devices?
You might be able to work around it by using an alternative bootloader for your “main” OS, such as GRUB or refind. This is at your own risk however, so make sure to do your research first before playing around with bootloaders.