I agree the the actual limiting feature is that your spy has to have full movement points but I get the feeling the point of this feature was to make sure you couldn't conduct a mission in the city the turn you moved into the city, probably to represent the need for the spy to spend a bit of time in a city before it can carry out a mission. So perhaps the devs missed that unloading a spy from a transport doesn't count as moving a spy.
Consider this strange example. Suppose there are two coastal cities - one owned by me and the other by my rival with OB. Suppose also that a transport can go from one city to the other in one turn, and that a spy on the ground can go from one city to the other in one turn. If I were to take two spies, send one by land and send one by transport to the rival city, only the one in the transport could conduct a mission right away. Also I'm pretty sure this would mean that on the following turn the transported spy would have the -10% for stationary spy while the road-running spy would have 0% still.
In this light does it not seem a bit odd?
I think I would tend to agree this is a feature but it's fairly awkward the way it's implemented IMO.
EDIT Actually it turns out the spy in the transport in this example has moved because he was loaded into a transport. But if you consider the same example but with the travel time being 2 between the cities then the point still stands.