I usually don't use specialists as they're not very efficient, but if you use then, then yes, you should of course factor them in. I suppose an easy way of finding out how close you can build your cities is to look at your empire at the end of a game and see if there's a big amount of unused space. If there is, well, then you could have built them closer to each other.
Beyond Earth is a lot different to Civ 5 in that regards. As I said, basic Tile yields have rather little influence long-term, so it's not about spacing out cities to not share tiles. Quite the opposite, it's a good thing to squeeze them together as closely as possible without running out of space for your citizens, because that means that you have less territory to defend, less spread that may annoy the AIs, less Maintenance for (and less time spent when building) Roads/Magrails, an easier time covering most of your tiles with satellites, the Ability to reach invaders with Air Units stationed in other Cities, more space for additional cities later on, etc.
You just have to make sure to leave enough space so every citizen has a tile/specialist slot available, because if you end up with unassigned citizens, then that's a much bigger problem than having cities spaced out a bit too much.
Oh and never take the AI as an example.
It's bad and very inefficient in pretty much any aspect of the game.