I cleared my FO3 install, downloaded MO2, set it up with NXM, downloaded both archives, installed them, sorted the plugins, and ran the game with FOOK2 active. Delete and redownload or maybe go to MO2 File>Install Mod>yourfile and see if that works. MO2 was an unexpectedly pleasant experience.
The mod does not seem to be packaged incorrectly. Does Vortex require mods to be repackaged differently?
The issue with old FOMM and 32bit NMM was that they could not extract the 2GB+ FOOK2 Main BSA. 64bit NMM (and FOMM Fork?) did not have the same problem.
EDIT: Uninstalled MO2, downloaded Vortex, set it up with NXM, downloaded both archives, and installed them. Found an issue where Vortex treats both archives as the same version of the same main file. Only one can win unless you make one archive a different instance. Any mod with multiple main files (presumably with the same version) will have the issue since updating is done by version. Enabled the plugins, sorted the plugins, and tried to run the game. Found another issue where Vortex was loading fose_loader.exe when I had already used the anniversary patcher. Have to make fallout3.exe the primary or have fallout script extender the primary and change the target to fallout3.exe. Ran the game with FOOK2 active.