I can think a reason, if the one unit per tile means that a rival civilization with open borders with you can block your movement by placing their units in your territory. It would be very annoying, if for example you could not move your worker (if workers are still used for that purpose) to improve some tile with special resource, because there is some unit blocking your way.
Or consider a situation, where you at war with some other civilization and you would need to move reinforcements to the front, but you are not able to because another peaceful civilization has some units in the way. If you could not start war with the other civilization as well (perhaps the two enemies would be too much to handle at the same time or there would be some other reason) you just had to watch powerless, when you loose the battle at the front.