I reinstalled the game today after several months, all Workshop content downloaded with no Issue. I launch the game through Alternative Mod Launcher (as previously) with no conflicts, all mods detected and active...

...but within the game the mods aren't working: the music is all regular XCOM 2 OST (and I use Music Mod System with several soundtracks installed), and when I tried to create a new character, all the customization items from Workshop are don't show up and the advanced options (legs, shins, etc.) don't show up at all.

WTF?
Do I need to launch the game normally first? Because I did and there was no difference.