I guess its trial & error. Got myself some small mods (like no pixelation & re-introduced cruise control) and that works.
edit: Ok, I read a bit into it. Its apparently a supermod in the scale of the Gentlemen mods of SR2&3. SR4 modding lean more into steam workshop stuff so I guess it might depend on files from the steam version since it was never thought of by the modders to do it without (an probably not possible to mod some stuff without) steam.
You might ask for help in places like this
but do not expect them to have a workaround; my impression is that they are shellshocked by a legit non-steam version of the SR series.
edit again: after skipping above linked thread to the last page they already waved the white flag towards the gog version :/