For now, the User Parameters is a part of the diagram. You can't make the SFX with the User Parameters but without a diagram.
However, you can implement the some sort of receiving a simple "parameters" in your diagram during it operation and save them into EEPROM.
In this case, parameters data input can be organized using a discrete button on CANNY inputs, CAN or UART messages.
Returning to SFX:
An SFX does not contain a diagram, but its binary code. Hacking SFX will require some effort. For that matter, even microchips are hackable.
Each device instance has a unique 32 bit ID.
You can link your diagram to a specific device ID.