After some good nights rest, my mind wandered back to the claim I made previously about Fallout 4 not being moddable with Vortex. Seeing claiming people they have had success on ProtonDB, I went back and spent a long while figuring it out. Now I present you this knowledge if you may need it.

Starting fresh

Start by obtaining both SteamTinkerLaunch, listed here, and a copy of the game, not listed here. Link the copy to Vortex as you would on Windows and set up as instructed. Once you have your staging and main folder set up, drag in a drop any mods you please.

If you run the game as is, you will not see any mods loaded in. To fix this go to wherever Steam has put your Non_Steam edition of Fallout 4 (labeled typically by random numbers) Ex. below

The path should be

/home/YOURUSERNAME/.steam/debian-installation/steamapps/compatdata/2195060229/pfx/drive_c/users/steamuser/Documents/My Games

Having found it, open the Fallout4 folder and (if not present) make Fallout4Custom.ini and inside the ini insert this text

[Archive]
bInvalidateOlderFiles=1
sResourceDataDirsFinal=

Hit save and close the text file.

If you attempt to open the game now only the mods containing .ba2 files will load in.

Listed 2 images above Darker Nights should be making Sanctuary much darker, however the only things dark in this image are Nora's nipples.

The Fix: Making a text file

Return back to the Steam dedicated folder for Fallout Ex. below

In your folder you may or may not see plugins.txt. If not create it and load it with mods from DLClist.txt or UserDownloadedContent.txt Ex. below

DLCNukaWorld.esm
DLCRobot.esm
DLCworkshop01.esm
DLCworkshop02.esm
DLCworkshop03.esm

↑Official DLC/Files, Do Not Include↑
↓Non DLC Mods, Include these↓

CBBE.esp
DarkerNights.esp
DarkerNightsDetection.esp
Eli_Armour_Compendium.esp

Copy and paste into plugins.txt and add * before them.

Booting up the game will take a while longer, however it should all work as intended.