Tunnels just a waste of space?
Is there any benefit in having buildings connected by tunnels, if I can put other building in the same place?
The tunnels supply the electricity as a basic function but you do need the tunnels so that your colonists can get to the buildings and to allow for air ventilation. Ease of access is one of the factors affecting the colonists happiness that is displayed on the sub menu along with the pollution levels that can build up without adequate tunnels and air filtration support.
Sci fi 101
As a veteran city-builder, tunnels are basically another set of "roads" for me. That's a common thread I see in many city-building games: roads. Without them, your little people wouldn't have an easy way to travel from one part of the map to another (just like in real life). Plus, when living in a pressurized environment like that, it's important to be able to get around without having to wear an environmental suit and breaking your ankle on uneven ground outdoors. I've actually done this; walk to and from one of my community colleges with no sidewalks, and it's a pain! (Long story, you don't need to hear about it, and no environmental suits, though one time I had to wear a lot of cold-weather gear, seeing as it was the Midwest at the time, in winter).
The commute button is also helpful in this regard, because it helps me determine where to put new habitats and skyscrapers for incoming colonists. Still, I really think long-distance transportation would be super-helpful in this regard. Even with careful city planning, there's gonna come a time when public transportation is needed to compensate for greater stretches between buildings.
Yes, I found it now in "happiness" panel for a colonist. Maybe it should be explained that there is a difference to travel through tunnel and a building.
Yep, we've added some stuff to the Commute overlay to make this clearer when you don't connect buildings with tunnels.