Hi there!
I received some feedback now, hopefully this will help.
So turns out I was a bit behind in versions, the r.NGX.Enable is now read-only after initialization starting with UE 5.1.
But also starting with 5.1 DLSS does not use r.ScreenPercentage at all anymore to change scaling factor. And it definitely does not do it through “SetByConsole”.
So what I am told that a possible root causes to what you are seeing could be that you still have a pre-5.1, deprecated “Set DLSS Mode” BP node in your project. But still DLSS does not override the priority of anything, so the fact that you are seeing “SetByConsole” means that something outside of the DLSS code must have set it.