I was wondering if wemod can be directed to launch the game via the Script Extender launcher instead of the steam launcher so that installed mods are still active?
It is coded that WeMod detects games from specific libraries on your hard drives, so it’s not possible to change it to be able to launch any game from outside of these platforms (Steam, GOG, Epic, etc.)
However, you can always try launching the game through the Script Extender launcher first, then click the Play button in WeMod after the game fully loads. Give that a try!