As far as I've seen that some cities are closer to the railroad or train tracks is not a big deal. The thing is that some cities are better focused in tourism, production, research, trade which leads to the most isolated one near the mountains which I believe would be ideal for resources and production wouldn't be in need of much tourists so it's less accesible.
The way I see it is giving the little cities something different to specialize in and are giving some perks and disadvantages to keep it balanced, some have more resources(mountain), water supply(near sea), dense forest to manage underground pollution, more ways to acces the city for tourism or commercial(video). It would be brutal if you settle a commercial city in the mountains though.
Besides every town has a way to connect with the outside world, some have the road others by sea transportation or train. and everyone has a chance to make planes, which are different from the international airport.
About the density in the video of a few hundred making skyscrapers its not a problem since is just balancing some numbers and done.
The only part that is bugging me is that there is a limit of how many great works a region can have.
