1. What happened
When we load a model from an AssetBundle the model does not show unless we re-apply the shader.
We have created a 3D cube and applied the "Mixed Reality Toolkit/Standard" shader to it. Then we created a prefab from this and then made it into an AssetBundle. We then load the AssetBundle, instantiate it and we can't see the cube. We can interact with the colliders for the cube, we just can't see it. Then we go through the models materials and re-apply the same shader and we can now see it. I believe we shouldn't have to re-apply the shader to be able to see the model as it already has the shader.
This only happens in the HoloLens 2 Emulator (not sure about the HoloLens 2 device as we don't have one yet), we can see the cube correctly in the Unity Editor.

2. How we can reproduce it using the example you attached
File > Build Settings
Universal Windows Platform
Target Device: HoloLens
Architecture: x64 (for emulator, ARM for device)
Build Type: D3D Project
Target SDK Version: Lastest installed (10.0.18362.0 for us)
Minimum Platform Version: 10.0.10240.0
Visual Studio Version: Latest instaled (Visual Studio 2019 for us)
Build and Run on: Local Machine
Build Configuration: Release
Copy References: false
Copy PDB files: false
Development Build: false
Compression Method: Default

Build to desired folder and open the Visual Studio solution file. Build it and deploy to the HoloLens 2 Emulator (version 10.0.18362.1042).

Run the app within the emulator, the app is called "ShaderBug".

Click the button "Display normally" and you will see nothing, this loads the AssetBundle without re-applying the shader.

Click the button "Display changing shader" and you will see the cube, this loads the AssetBundle with re-applying the shader.

3. Notes
Reproduced on Unity 2019.2.15f1 and Unity 2019.2.16f1. This bug was not present in Unity 2018.4.12f1 or Unity 2018.3.0f2
Reproduced on HoloLens 2 Emulator versions 10.0.18362.1042 and 10.0.18362.1034