This issue came up on discord again. Looks like the issue is that in the knossos mod.json file, the mod_flag section which specifies load order doesn't have an entry for the MVPs. Add that in, it runs again. Lots of warnings though. The other problem is that by default Knossos thinks the last number in a version requirement is harmless bugfixes, so while the file specifies BPC 1.0.6 it will load the latest 1.0.X it has, which is bad. I can hand-edit it to require 1.0.6 but I bet it needs a specific MVP version too to work right.
If someone can tell me which version is stable for this mod(EDIT: I did the smart thing eventually and read the first post, will proceed with 3.7.2) , I can punch that in and attach a mod.json file for future players to use. It's not ideal for people to be messing with that themselves, but if the mod isn't working to begin with, I don't see much harm.
EDIT: Attached now is a working mod.json inside a zip file. Extract that file and put it the directory knossos creates for FriendsandFoes-1.1.1. In order for this to work you will either need BPC 1.0.6 and MVPS 3.7.2 installed already, or you will need to tell it to download them manually. You can this by finding each mod in the explore tab, clicking the "DETAILS" button, and then using the dropdown menu near the to left to select a specific version. Then even if you have a more recent version the install button will become available. Use that to grab each, and once they're downloaded you should be able to launch Friends and Foes.
Be sure to restart your knossos after putting in the new mod.json file or the changes won't take effect, though.
The result still generates some warnings in debug mode that are a bit concerning to me, but I don't have any familiarity with the mod so I can't take it further than that.
EDIT 2: See Mito's post below for a more complete effort.