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It is the other way around. Mod Organizer 2 is the better one, as Vortex will mess up your game and install mods incorrectly.
MO2 can handle perfectly each mod, yes also F4SE. Heck, it's even based to work along with F4SE. I use MO2 myself and also have installed F4SE (no, not through it, as you install f4se manually). I run the game through MO2.
Next to F4SE i use MCM, LooksMenu, CBBE, HHS and several armor and clothingmods such as vtaw wardrobe 9.
I used NMM, Vortex (kind of successor for NMM but much more elaborated and complicated) and Mod Manager 2 over the time. Only with NMM I never ever had any problems, despite many Inet warriors informing you for years about NMMs big failures. Both Vortex and Mod Manager 2 gave me some headache a few times, but it's manageable.
NMM is outdated, since some time I use mainly Mod Manager 2. I have 192 mods installed, not a lot by the standards of many. A bit difficult to get into Mod Manager 2, watch tutorials, but it is worth it, as it is a great tool for easy management. For me it's easier to understand than Vortex. It's great that you can use F4Edit (mandatory for mod control) and Body Slide/Outfit Studio through Mod Manager 2.
To F4SE: Many interesting mods need F4SE, a script extender. Many people have problems with F4SE, but it's easy to use and should always be installed manually. Just unpack the mod (with the free 7z for example) and copy the ingredients to Steam/.../Fallout 4, where the FO4.exe is (not into the data folder). With Mod Manager 2 you then would create an executable for F4SE, it's easy and fast, but first time you have to look a tutorial on Youtube for this. You then always run the game through F4SE from Mod Manager 2 (and no automated updates have to bother you).
I wouldn't recomnmend F4SE be installed as a mod.
Why, you might ask?
Because it isn't a mod, it's an executable just like fallout4.exe is. It should be installed into the same directory so it can run natively.
It does have a DATA sub-directory contain script files but again if you want the fastest possible and reliable execution it means extracting it into the main fallout4 folder.