We'll I'm experiencing the same issue, unless you run a mega factory where you have enough room to build several production chains next to one another.
In my case, I built a wall right next to the miner, to keep it outside of the building, but even power poles or elevators close by don't like those hitboxes. Even if you have plain visual sight that nothing is touching, you get the "not enough clearance" message.
In given situations, were you are bound to building structures tightly next to one another, this would definitely help out.