Both programs do the same thing with regards to the Patch, only TESVEdit does this manually (the set up part), where Bash uses Tags to make the process easier. FNVEdit does require more knowledge of mods and leveled lists and how they affect the mix so that one can adjust things as needed.
I prefer Bash myself as the last time I tried to tweak the Merged Patch it was not pretty, where as the Bash Patch is much easier to implement. I also prefer Bash as I can do some tweaks on the Patch itself, so I don't need a mod for those, thereby cutting down on my load order. Perhaps these tweaks can be applied in FNVEdit, don't know, have not dug that deep into that part of the program. I use it to clean mods mostly.