Don't expect too much from me about the masterkey.
I suspected many different process to boot 3.60+ Games on older firmware and also some other stuff related to the internal emulation (PSX/PSP/PS2)
Have many theory about the dongle but i'm gonna explain something.
1-Many Official Game had standart self renamed to EBOOT.BIN (not even npdrm) you can easily unself them (and fix the encrypted section)
2-Patch the header from the official eboot.bin -> (self) and they don't make own eboot from this way, they patch the header to be work on a 3.55 Special CFW (allow to load specific stuff related to the CELL Execution)
3-the dongle = emulate debug patch dev_flash/payload that allow to boot into the debugger mode -> also to patch in real time (syscall function between usb port/CELL) remember jig generate dongle id
4-also some PS3 Games use specific SDK revision (like i show on a another topic)
5-and for the eboot NPDRM is different -> lv2kernel related to the liblv2.sprx, etc patching it's your answer