There's whether you should be able to run your own code on your own device, which I think most people here are on board with.
Then there's whether you should be able to misrepresent what you've agreed to ship through someone's network when you've presumably signed contracts and made statements about that end up being untrue. I think most people would agree that Nintendo should have the ability to control what they allow in their store.
Finally, there's how these interact, because you can only really run stuff on the switch that Nintendo allows in their store, which makes the issue much more complicated.
Which part of the issue someone focuses on will likely inform how their comment is formed, but also how they interpret other people's comments, whether they are really focusing on the same aspect of the issue or not.