Its an easy way trying new mods and removing them after if you dont like them or they break the game. I personally have a couple of overhaul mods for skyrim that dont use the manager but all the others I use do. Agreed also some mods do not work with mod manager but a lot do. I agree its not the best way to do it but it is the easiest and thats what was asked for, yes you do need the SKSE with some mods but like i mentioned, read the instructions the come with the various mods, the links a for extra files ect are usually in there.