That is a good question, and I don't know how it is done. These are guesses.
1/ They might have a record of the ID of last box that the card was paired to, AND was working, and the replacement card will only work in that box. If that is how it works, then the OP information is correct, the replacement card would not work in another box. I think this is unlikely, too many complications for Ѕky.
2/ The replacement card does pair itself to the first box it is used in, but pairing goes on in the background, and no messages are displayed on the box. If this is the method, then the replacement card could be used in any box, but once "paired" would not work in any other box.
When the replacement card is put into a different box, it goes through the familiar routine. It asks for pairing, and displays "Pairing successful, please wait" onscreen. Premium channels never clear - although base channels (eg Eurosport, and many others) do work.