@OldSurferDude I am not sure what the real difference between c/c++ code with the Arduino libraries, and c/c++ code without the Arduino libraries. But I don't think there is much difference. it is still code, and it is possible to add other libraries as well. So if your code needs any libraries, you should be able to include them like you would normally do.
From what I understand, the MySensors hardware abstraction layer for rpi includes an emulated EEPROM. So you can use the Arduino EEPROM stuff if you want to, or just use plain c or c++ code to write to a file.
For nodes, it is possible to force node id by setting MY_NODE_ID. However, a MySensors gateway always has node id 0 so this is not applicable for a gateway. You would not need to write any code that saves and restores the node id.