I don't know, which is why I was vague in my reply. It's not something you can just quickly change with zero knowledge.
https://github.com/gluck/il-repack
Merging the assemblies after build might be fine to do, but again, I do not think you need to do this. Plugin files really should be kept as separate files.
24/03/10 - New Update:
Legality: Added Encounter Slot RNG correlation checks for Gen4 (and Gen3). Because Encounter Type PID mismatch wasn't enough!
Gen3 correlations are complicated by vblanks, so with PKHeX's default settings it does not raise a flag. Basically, the program tries to check the encounter conditions (if you need a specific lead), and indicates if it is unable to determine how that frame was encountered.