The short story:
I was going to post in the MO2 support forum, but it says to only post questions in there dealing with FO4 and SkyrimSE. Does that mean MO2 isn't recommended for other games? I'm having a problem with MO 1.3.11 so I "upgraded" to MO2, which fixed the problem, but INI Tweaks aren't functional in MO2.
The long story:
I started a heavily modded game of FNV over a year ago using MO. I've taken a breaks and come back to it off and on. It has been a long game and I still have lots more to go (366 hours so far according to the save). I was planning to resume my game this weekend, so I fired up MO last night to check for mod updates. There were a few, so I downloaded and began updating them. When I tried to update JIP LN, which uses a FOMOD script, I got an error: "Unable to obtain public key for StrongNameKeyPair; installation failed (errorcode 5)." I tried to re-install the old version, but I got the same error.
All of the other mods installed fine, but they were just loose files where the JIP LN has a FOMOD script in it. I tried installing another mod that is FOMOD scripted and it gives the error too. I had no problem just a few months ago, and the only thing that has changed was MS managed to sneak the Fall Creators Update on my system, so I think that update broke something.
Searching for a solution I found this old post that was pretty much what was happening to me, except I'm installing mods for FNV. I tried the suggested solution linked at the bottom, however the beta version 2.0.7 wouldn't install. It gets to a point where it looks like it's trying to download something, but after a minute or so it gives an error and doesn't install. I couldn't find a stand-alone package for the beta versions, which I prefer. I tried downloading the fix anyway and dropping it in the MO 1.3.11 directory, but it still wouldn't install JIP LN. It didn't pop up an error, but in the log window at the bottom, it said "no files in installed mod."
I was reading another post somewhere with the same problem and someone mentioned MO version 2.1.1 working for them, but the latest version I saw was 2.0.7 beta. Searching 2.1.1 lead me to discover the stable MO2 release is on SkyrimSE Nexus. I didn't even know MO2 had come out of beta because all of the links to download MO on the Wiki here lead to the MO page on Skyrim Nexus which is MO 1.3.11, and there is no mention of MO2 there either. I knew of the beta versions, but I there hasn't been an update to them on the GitHub page in almost 2 years so all this time I thought MO had been abandoned.
I install MO2 and it works. I got all of the mods updated, but when I ran it, the fonts were messed up and the mouse acceleration was back (all of which I had setup and fixed with INI Tweaks). I checked to make sure my INI tweaks didn't get disabled in the transition, and then I saw the INI Tweaks box grayed out with "INI Tweaks *this feature is non-functional*" above it!
I tried replacing NCC directory in MO 1.3.11 with the one from 2.1.2, but it too gives me the "no files in installed mod" error when installing JIP LN.