Mod Anthology is for accepted (or dropepd) mods. SPERG is not in the Anthology, instead it is in 'Mod' section.
You can use SPERG without any of the packs, no problem. Might have to do some minor conflict resolution here and there. Might be good to ask the question in the New Gameplay Overhaul thread in the packs section, those guys can help you best.
It shouldn't make a difference because MO uses everything in your /Data folder and overwrites (by means of a virtual drive) it with the things you put in MO ((I think so at least, I have a clean Steam version of Skyrim in /Data so can't tell from experience). Myself I use the MO variant. In MO, I have a mod named SKSE and within that mod is a folder named SKSE. The SKSE.ini file is placed inside that folder. Sounds like you already have that though, if I understand you correctly, but double check to be sure.
Some questions to get more insight in the situation:
1) You are launching the game with SKSE, I assume? 2) Do you encounter SKSE script-related errors in your game? 3) Are you really sure the file is called SKSE.ini? In windows you need to enable showing file extensions somewhere, otherwise it just creates a *.txt file but will still show as SKSE.ini as file name.
If you did all that, well the SRLE instructions are rather clear so I would verify ( once more I guess) that you have done what is mentioned here https://wiki.step-project.com/User:Neovalen/Skyrim_Revisited_-_Legendary_Edition#Script_Extenders and here https://wiki.step-project.com/User:Neovalen/Skyrim_Revisited_-_Legendary_Edition#SKSE.ini
