I'm not sure where you draw the line for this, but last time I went into Switzerland I had my passport checked at the border.
That's because Switzerland isn't part of the Schengen area
That's wrong. Since 2008 Switzerland is definitely part of the Schengen area. While the UK is not.(https://en.wikipedia.org/wiki/Schengen_Area)
So if you fly in from the UK (or any non-Schengen country) you need t show a passport. As is the case in any other Schengen country.
And random checks at the border are permitted (i.e. contraband, people trafficking).
Also a country is allowed to re-implement border controls in case of crisis.
And how exactly do you show that you're a citizen of a country in the Schengen area without showing a passport?
I think that's the case in most Schengen airports now.
What can happen is that you're checked by customs at the border. Since Switzerland is not in a customs union with the EU. Generally speaking, though, it's free flowing.
Legally, referendums in the UK are advisory only.