• Create new 3D project
• Add several different model primitives in 3D view
• Assign each model a different material from content library
• Add all models to content library (User 3D section)
• Create new 3D project
• Drag all added models one by one from content library to 3D view
• Toggle "Show only visible components" in navigator

--> Some of the nodes will be hidden in navigator, though all should stay visible

There should be no functional difference between some of the nodes that stay visible correctly and the ones that do not stay visible.

The ones that are hidden have incorrect "visibleInNavigator" trait.

What happens behind the scenes when you add a model from content library to the scene is:
Two qml files are added to Generated.Bundles.User3D module, one for the model and one for the material (e.g. MyCone.qml and CarPaintMaterial.qml). The types are also added to qmldir file:

MyCone 1.0 MyCone.qml
CarPaintMaterial 1.0 CarPaintMaterial.qml 

Materials have additional resource files (images and shaders that are also added into the module subdirectories) but these should not be relevant for this issue.

This behavior seems to depend on the material that was assigned. It seems that if the material type name is before the model type name in alphabet, this issue occurs, but if it is after, this issue doesn't occur.

So looks like the issue might be that when more than one types are added to a module at the same time, only the first one alphabetically gets traits properly initialized for it from prototypes.