My set-up:

Win 11, nearly brand new MSI Laptop
i9 14900, RTX 4090 (laptop version), new SSDs

I had this same issue on my previous desktop

I use Vortex
One tab of F4SE is pathed to the Steam FO4 game files and one is pathed to the GOG game files.

When I try to open identical mod lists and moce save game sot test the GOG game has messages about dozens of missing plug ins.
yet those mods and the plug ins ( ichecke dseperatly) are all active.
The game just doesnt see them.
I just did a new game start and whichting just a few minutes found multiple mods not showing up in game:


-Select Assault Rifle, the hatch to get it did not exist and a console command search drew a blank also

-Select Power Armor, The hatch to the basement to find it did not exist, a check via console command search same result , not in game

-jetpack integration into Power Armor legs. not in game

- Diamond City Security buff, not in game despite active in mods and plug ins

- Xander's Aid (big Quest mod) enabled both mod and plugs ins. - no show in game

-Clothing replacer I had forgot about. I noticed this time since Pipers outfit looked less sexy, so anotehr one not in game

-Diamond City plus (a DC Expansion) - no show in game, despite ative in profile in both Mods and plug ins section

These are the issues I always had with the GOG game on 3 different computers and at least 3 maybe 3 versions of Vortex now. All on Win 11 (not sure if it matters)

Someone onece told me thete is a "trick" in the game files somehwere somehow? to make GOG activate those plug ins?
Vortext was properly pathed to the GOG game or the mods I did use ( such as Cheat console to teleport me around to check the modded locations) would not ave worked either.

Any ideas?

I think the problem is having a Steam install and GOG install.

I've had zero issues just following the standard instructions to get Mods working with Vortex. But I ONLY have the GoG install.