I guess it is 1.3 limit. It probably keeps looking for first "bootpoint" (bootable HD) device but does not check if there are more when creating list of bootable devices. (Floppy drives use bootblock booting and are handled separately)
Directory harddrives and hardfiles from Amiga point of view are two different devices (they use single autoconfig board but only because it was easier to implement)
Perhaps it is possible to reorder devices depending on boot priorities or something. Did you try moving hdf above the directory drive on harddrives panel?
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