So I decided to write my own "patcher" myself in Python (sounding like a good idea as NMLC already needs python), and since I think I've made it robust enough I believe I should share it with the community!
Download link!
I'm distributing it under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
So far it can read references from pnml files (#include "example.pnml") to patch together and use custom variable definitions for reference in the code (#define CUSTOM_DEFINITION 288).
The rest will just be written directly to the nml file to be compiled.
The definition does NOT currently work with function-like definitions.
Please give any feedback, it is much appreciated

I hope you enjoy!
Edit 26 05 18: Use the download link above, includes full example and license