MO works fine, with one or two provisos:
Don't have any of your games installed in any UAC folder in Windows or any tool called from MO.
Turn off ALL ingame overlay software from any manufacturer, Steam, AMD, NVidia, Overwolf (not sure on the actual company name for that last one.)
The actual mechanism that MO uses to provide the virtual installations of the mods is very similar to that used by malware/viruses and as such your AV software may need to be told to exclude it from checking. The initial project was part of @Tannin's university doctorate into malicious software and started life as a 'proof of concept'.
Aside from that, MO is a great platform to mod your game.
One last thing, there have been reports that Windows latest "Creator Update" has completely broken MO so you may want to consider that also. I have not got that update yet so I can't check.
