I figured it out - you need to make sure your game has no launch options enabled.

Mine had "-windowed" and once I removed it, it worked

I have the mods (and the Playable Factions expansion, which is recommended to be loaded at the top) installed and loaded in the load order of the mod manager - I checked the load order and have ordered them from top ([TROM + TUP] Playable Factions Expansion [1.7.2]) to the bottom (HITCHANCE VISIBLE). They have also been activated. When I click PLAY, it shows me that I am playing with all the mods as loaded.

Yet in the main menu, when I go to New Campaign, I don't see any of the new content. The playable factions list is the same as it used to be across all the starts, and when I tried starting up a Liu Bei campaign none of the portraits of the generic generals have been replaced. Could someone help me understand what I'm doing wrong?

I was wondering if it might be something to do with my DLC being loaded in - I have most of the DLC but not all already installed.