I had to learn to use MO2 as part of playing Fallout 4 since FOMM didn't handle it, but once you've learned how to use MO2, it becomes your preferred mod manager for all the older games as well since it's so much more powerful.
MO2 has automatic handling of archive invalidation, coupled with the bsa settings in the FalloutCustom.ini file, so archive invalidation never needs to be worried about. Sometimes after installing a mod via FOMM, you need to toggle that to get the mod files working. FOMM also has a setting to manually toggle archive invalidation on and off. This means that it's super easy to remove a mod later - just remove it in MO2 and it's gone without affecting any other mods. Nothing is overwritten, just not included as part of the virtual folder when the game runs. MO2 makes a virtual data/ folder, and uses the priorities you assign mods in the interface to determine which mod will "win" when files conflict from one mod to the next.
It also makes it harder to uninstall mods as you need to manually delete mods and rewrite any files that mod had overwritten. FOMM installs everything into a physical data/ folder, so depending on the order in which you install things, files will wind up being overwritten, which can possibly result in problems. I used to use FOMM, but you have to manually handle mods overwriting each other.
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