There are Slot-1 ROM emulators. They're called "flash carts". Those work with a high degree of compatibility.
nds-bootstrap works by patching Slot-1 accesses and redirecting them to the nds-bootstrap code, similar to how Nintendont redirects disc access on Wii. It's not perfect, and it's slow because the SD card can only be accessed by the ARM7 CPU, whereas Slot-1 can be accessed by both ARM7 and ARM9.