The other incursion you may be thinking of was at LAX but involved closely spaced parallels and not crossing runways.
Incursions and their prevention is a hot topic here too.
Transport Canada and
Nav Canada have lots to say on the subject.
The use of "taxi into position and hold" is also mentioned insofar as aircraft should not be allowed to line up on the runway if there will be a delay to their departure. 3 minutes is a recommended maximum and the instruction should include the reason for the delay and the anticipated length of the delay. Seems much more common sense than stopping its use altogether.
In relation to the ORD incident, what was the trainee's instructor doing? It seems the conflict was spotted by another controller not the trainee or their instructor. Troubling.