In the case of the bridge, I suspect that while the original design probably looked fine on a 2D screen, in VR the view looked like crap, so they expanded the size of front window.The top one was designed more or less correctly to scale. The cockpit is fairly normal-sized in relation to the figure standing there, and it immediately gives a proper sense of the size of the ship.
Compare it to the ship we got:
View attachment 224439
They don't look anywhere near the same size. It's that cockpit. For some reason they made the Clipper and Cutter cockpits huge, like comically huge. The Cutter's cockpit window is as large as a modern jet fighter.
You might be right that instead of upscaling small ships they actually modeled them as large ships, but they still made critical features too large and someone signed off it and that's what matters.
I still think they upscaled the ships though and added the seats and instruments after.