I think you're misinterpreting what psychotrip is trying to accomplish. He isn't having a problem installing and running F4SE or MCM, rather he's having trouble with mods that utilize MCM showing up in the actual MCM menu.
If you wanted to test this out, simply get a clean install of Fallout 4 - install F4SE and MCM using Mod Organizer 2 (latest version from github), then install a mod that utilizes MCM (such as Extended Dialogue Interface or FallSouls) and it should show up in the MCM menu when in game. This is not the case, however, as the only things that show up in the MCM menu is "MCM Settings" and "Hotkey Manager".
So, no, Mod Organizer 2 still hasn't fixed the MCM issue and you would still have to follow the methods the OP posted. I am still having some trouble with some MCM interfaces even after doing the fix, so it's more of a band-aid on a gunshot wound until someone decides to actually fix the issue.
If anybody else has made any progress with this issue, I would love to know any workarounds because I'm on the verge of giving up on MO2 and just going back to NMM.
Edited by dev614, 19 February 2018 - 04:14 PM.