Hello Sheson,
thanks for the information! I moved dyndolod from skyrim modding tools folder and into it's own area and got it to work, but using the standard skyrim file path didn't load any of my mods. I managed to get it all to work with:
-sse -p:"C:\Games\Mod Organizer 2\profiles\My Skyrim Profile\plugins.txt" -m:"C:\Games\Mod Organizer 2\profiles\My Skyrim Profile\" -d:"C:\Games\Skyrim Anniversary Edition\data"
loading my mo2 profile for plugins and ini files completely worked, I guess I am just confused why you shouldn't point it there since mo2 completes a completely separate game in a way. Non the less doing those arguments fixed my issues and I was able to get it all to work as needed.