You need to be very careful in merging mods with scripts or that require a script extender, as there may be references in the scripts that expect parts of the original mod to be present in their original forms to work.ba2 files that come with the mods you want to combine into their loose components and correctly combine those loose components manually in the correct order so that the overwrites match the order in which you merged the mods (Merge Mods may do this automatically now, I haven't used it in a long time). The downfalls, however, can be significant: In terms of benefits, the main one is reducing the number of. There is a script for FO4Edit that can do it, and a separate program called Merge Plugins that does something similar.
There are, indeed, a couple of ways to combine mods.
