As for leveled lists, I am inexperienced with these matters, but wouldn't they both alter, for instance, the Talon Company or Supermutant leveled lists?
They do not.
FEV does indeed make changes to some vanilla leveled lists (Supermutant1WeaponGun, Supermutant2WeaponGun, Supermutant3WeaponGun, Talon1WeaponGun, Talon2WeaponGun, Talon3WeaponGun, ...).
In all these cases FEV removes all entries from this list and instead adds a single new entry which references a new leveled list, e.g. FEVLevelistSupermutant1Guna [LVLI:06003031], FEVLevelistSupermutant2Guna [LVLI:06003030], ...
FOOK doesn't touch these leveled lists at all. The main battle field is in the inventories of the Creature records.
Here both FOOK (always) and FEV (most of the time) remove all existing entries and instead add a single entry referencing a leveled list.
e.g. for CrSuperMutant2MinigunA "Super Mutant Brute" [CREA:00092C4F], both remove the WithAmmoMiniGunSupermutant [LVLI:0002F6FC] entry, FOOK adds XZXInventoryCompleteMutantLvl2Minigun [LVLI:05031249], FEV adds FEVLevelistSupermutant2BigGun [LVLI:06003037].
Both of these level lists then spread out in a whole hierarchy of more leveled lists (but differently structured hierarchies in both cases).
So a leveled list merger isn't going to help at all here.
Now, you could be asking for an inventory merger instead. But what could it possibly do here? It realizes that WithAmmoMiniGunSupermutant gets removed, so it will remove that from the final merge result. It realizes that both XZXInventoryCompleteMutantLvl2Minigun and FEVLevelistSupermutant2BigGun get added, so it adds both of them into the final merge.
But both of these leveled lists will expand into a complete inventory, so your Super Mutants end up with a double inventory, once according to FOOK and once according to FEV. That's not really going to work well, is it?