PiStorm Musashi emulates a fake autobooting SCSI card for it's HDD called PiSCSI so the internal IDE controller of the Amiga 1200 Gayle should still function.
PiStorm Emu68k has drivers for the RPi eMMC or SD card controller which is puts in an boot ROM aside from Kickstart. The internal IDE controller should still function.
As to how to select boot priority I don't know.
I'm with Nor Bert possibly a clash of HDD/partition names?
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