Project being built as a 2D window, and not as a 3D environment in HoloLens 1?

The problem
As a follow-up to the issue presented here, we managed to build a working HoloLens app using MRTK v2 RC. However, the built solution isn't exactly ideal. As the title suggest, what we see is a 2D window (showing the Unity splash as hoped, and proceeds to open the project) but not an actual 3D environment. Furthermore, it shows the Developer Console, which we deliberately have NOT asked it to in the build options. It seems like some code is run, that we don't have control over?

Images illustrates the issue at hand:

The error-message
I'm unsure if the images are too small to read the error code, in that case (and in case it's relevant) here's what it says:

A scripted object (probably Microsoft.MixedReality.Toolkit.Input.MixedRealityInputSimulationProfile?) has a different serialization layout when loading (Read 76 bytes but expected 300 bytes)
Did you #ifdef UNITY_EDITOR a section of your serialized properties in any of your scripts?

What we tried (and discovered along the way)
As previously mentioned, this is a follow-up to the issue in which the app would not at all run on HoloLens. The solution to that, (or what we tried and what worked right after) was to open up the HandExample (as seen on above images) and use that to get started.

Now where it gets mysterious is that after this we made a completely new project, with only a SampleScene and the MRTK, and despite no difference from the last time we attempted the same thing, we still get the window to open, even though this previously resulted in an app that would only build and deploy, but not even open up. (Note: Above pictures are only different scenes within the HandExample, but the new project acted the same way)

On below picture you can see our built settings and XR settings. (Potentially relevant as they have previously been mentioned in relation to these issues?) Also please do note that Development Build is NOT ticked, but still it behaves as if it is.

What we want
It's a great starting point that the app actually builds and deploys to HoloLens now, (yay) both with and without the examples, but it would be neat to see everything as a 3D environment we can move around in instead of just a 2D window.

To deploy a 3D app you need to enable the Virtual Reality Supported flag. In the list of Virtual Reality SDKs you need to add Windows Mixed Reality.

As already suggested in this answer the WSA Holographic Remoting Supported flag must be unchecked to avoid black screen when the application is deployed on HoloLens or on emulator.