Yeah, I emailed their customer support, and was told that at the moment, it's not possible to flash the program changes outside of what the MHD itself did. That's somewhat disappointing, but it does make sense for user protection. I was looking at MHD manual, and it does indicate that there're multiple write options you can choose for flashing a custom bin (full write, long write and map write), but sounds like it won't do anything for a custom bin with custom logic not done by MHD.
Anyhow, I'll try to use another tool which can write program area changes via OBD port, I don't want to remove the intake manifold and pull my DME out and write to it on the bench at the moment.
At the moment, I'm not planning to write anything interesting yet, just want to change a CCP CAN config. I want to see if I'm able to log any memory locations I want.