Not a trainer/mod issue. This is just a plain old, run-of-the-mill bug. Playing the game clean and have had this problem. As I am sure many others have as well.
The issue is clearly related to the dagger/ Wolf's Fang Asset. The game is telling itself that you do not posses it when you actually do. The reason you can still do the companion skills is because accessing those skills is not actually related to the dagger asset and is just an animation change from when the companion does it themselves.
So the question is what is the trigger that flips the "PC has dagger=True" to "PC has dagger=False" Because it would have to be this. If it were just the VISUAL asset not loading the alters and chest would still be interactable. It also seems to be mutable via world state which makes me think it Could be a holdover from a previous version of the game where maybe you could lose the dagger temporarily depending on choices. Or maybe you were meant to lose it's abilities when certain events transpired.
In any event while Trainers/Mods Can be an issue that can cause problems this is doubtful in this case as it's too widespread and clearly affecting non mod users.