Differences between .enl & .cfg files - PatPL/Generic-Engines GitHub Wiki
Generic Engines uses its own .enl (ENgine List) files to store engines in a format, that allows both saving and loading engines to the program. More about inner workings of the .enl format
.cfg files the used by KSP to load, among other things, parts. Generic Engines can't load an engine from a .cfg file. It can only export engines to .cfg file.