There's no way for the driver to know how many vehicles are in an occupied platform, only that it's occupied. The calling-on indication authorises him to proceed only as far as the line is clear, driving accordingly and certainly not making any assumptions about how many vehicles are already there. The collision at Norwich is the only one involving a move into an occupied platform that I can recall in recent history, and even there (although the combination was slightly too long for the physical length of the platform, it fitted from a signalling point of view) I don't think there was any assumption on the driver's part, just a loss of concentration.
Does the ARS at Leeds allow calling-on routes to be set automatically? In some installations, it waits for them to be set manually instead, presumably at least partially for this very reason. In this case, with the suggestion of a set swap, the ARS would probably need to be overridden anyway. That won't make much difference, though, if the signalman's unaware of the changes to the plan and doesn't know that the second train is longer than booked, if indeed that was the case here!