I am having the exact same problem.
From what I have gathered, the startup isn’t loading the packaged uasset data from the project.
I think Switchboard will tell you, if you are using it to launch the project, gives a yellow warning message that it can’t find the .uasset data.
I find this strange because I have used a third party program to view the packaged .pak and .ucas files and I can find my .ndisplay config within the pack.
I have done a TON of very exhaustive searching online, it sounds like the ndisplay config doesn’t even need to exist within the project itself unless you are wanting to have a blueprint that acts directly against it or if you have C++ code that is wanting to modify that specific ndisplay config during runtime.
I would imagine, if you pass the .ndisplay file to load from the command line (with or without Switchboard), Unreal loads a ndisplay config during startup and places that into the level based on the uasset or ndisplay file you told the command line to point to. But, if you do this, it still seems Switchboard complains about missing .uasset loading, which just seems odd.
I am currently playing around with hand editing the assetpath within the .ndisplay file to really determine what this option does. Along this, I am also going to try and search the engine code for ndisplay to see if I can get a handle on what is happening here.
The same as you, I am just not having any luck with ndisplay working for a packaged build. If I load the Unreal Editor up on multiple machines and use the .uproject file, I can seem to get it to run that way, but this is not ideal and can lead our specific use case to be difficult to utilize.