When I didn't need to worry about trains, I used to commute by MTB. At first I used the tyres that came with it, and they clearly had a noticeable 'thrum' due to the tread blocks. You could feel them squirming sideways and moving about. And the tread meant that the ride was bumpier and therefore slower than the same bike when I moved to something like a Specialised Nimbus (even though that had some tread pattern).
Obviously, the effects are reduced by less aggressive tread patterns, but all the issues will still affect a city-biased treaded tyre to a lesser degree.
Finally, the point about the contact area - there's been a big shift in thinking about this in pactice on the road.
Maybe in a smooth velodrome, it's correct to think that a hard, thin tyre is fastest, but what actually slows bikes down are the lumps and bumps in the road surface. So just like running knobbly tyres, but the knobbles are on the road, not the tyre. It's this road vibration that slows bikes down
Many road racers have found that moving from a 23mm tyre to a 25mm or even 28mm tyre (at a lower pressure) will offer significantly better (i.e. less) rolling resistance, greater comfort and reduced fatigue.
The attached video explians it far better than I can.
View: https://www.youtube.com/watch?v=yrHxQg1OW0A