For flashcards, their ROM loaders patches the ROMs to read from it's microSD card slot instead of the Slot-1 card's ROM chip (in this case, the ROM in the chip starts up your flashcard).
When using a ROM loader like hbmenu, the ROMs aren't patched, so the ROM attempts to read the Slot-1 card's ROM chip.
I agree, this is the problem, but I don't know what has been done to make progress solving it.
I know that there's been talk of studying how flashcarts do it in order to recreate that but I don't know if anyone's working on it.
(I feel like I sound like I'm complaining. I'm not at all, people are doing excellent work and making incredible things happen! I'm only asking questions because it's fascinating to me and I want to understand more )