I don't know how much you want to change FMP, but if it's just a few additional OXCE features, you can also just create a small FMP submod... no need to copy the entire FMP.
Yes I undertand. But is much easier to bundle it this way. Just donwload, copy orignal Xcom files, enable mod and play. Solarious went this way with Xcom files. Also not all players know how to install mods and where to set some options neccesary options.
And certanly it is easier to tweak it this way.
Also I can't find FMP on github (only it's outdated version). Maybe it is time to put updated version with some extensions. Maybe someone will fork it.