It really depends on the operator, but as you say the Express division has lower stats than mainline. I asked a management type once why we didn't hold them to a higher standard and he said it was not that simple, as there were good reason for the higher cancellation rate, as you mentioned in the ETD swaps. You are right, CAT II doesn't come in to play that often, but when an airplane operated 10 flights a day it can really hammer an operation for that day.
I have been on Express carriers that put the mainline to shame and Express flights that I was embarrassed to have US Airways on the side. the mainline, but in general mainline completion is better.