Although I am sure it is much easier to install vent stacks and chimney pipes immediately after sheathing the roof and before installing your roofing, I am sure it isn't always feasable to get this all done before hand. So..... do a large percentage of people end up cutting holes in their new roofing after it is installed?..... or is it imperative that these tasks be completed prior to the new roof install.
It is much easier to do a good flashing around roof perforations if the vent pipes, etc. are all in place before the final roofing is installed. Think the entire roofing process through before deciding to do something like a chimney flashing later. It is not impossible, just easier in many cases. depends in part on the roofing material and the type of flashing. Special flashing are available for metal roofs that do an excellent job after the metal is on, for example.