The MFDMMods can still run without the warning error if clear the strive for conquest 2 folder in roaming first, start with an older version of the game (itch post only says 1 year ago so not sure exact date for the older game version was available back then), setup the mods by starting the older version, turn it off after the mod works. Then, download the newest version of strive for conquest and start the game. If successful, the mod opinion in starting opinion screen would remain empty, however mods are activated and starting a new character would get the male human silhouette.
I'm unsure why it would run this way, seems not related to neither setting.ini nor mods.ini as I tested with these two removed and still work.