While modding FNF on Linux, I noticed that modchart.lua doesn't work on this system, I looked in the code and saw that it was done with #if windows is there a way around this? or should I wait for a ...

If you wish to disable things like Lua Scripts or Video Cutscenes, you can refer to the Project.xml file. Inside Project.xml, you will find several variables to customize Psych Engine to your liking.