If this is true (I have no reason to believe otherwise), then I consider it a failure on the coaching staff. Still don't see how it prevents Smalling from calling an audible and switching things up, but maybe then I'm asking too much from the limited fella.
Do you think Jose Mourinho is the type of manager who likes his players to go against his instructions?
We dont truly know if he is or isnt told before the match to mark a specific player who is their most threatening from set pieces. But if you tell your CB to do that and he doesnt mark that player, why would Jose Mourinho pick Smalling the next match? Someone who doesnt listen to his instructions?
Likewise, if Smalling "calls an audiable" and does what he thinks is best against the managers instructions he's going to be in the dog house there as well.
So if you are Chris Smalling all you can really do is what you're told, because even if its the wrong thing and costs your team a goal, the manager isnt able to blame you and leave you out for following exactly what he told you to do. Thats what he wants from his players.