In Plymouth, for PCB at least, the below takes place on many routes:
Typically in the morning, the service startup on selected routes that are single decker or lower frequency would have an increased frequency for the first couple hours, just before the school contracts start (around 0800), after which normal vehicle allocation and frequency resumes.
In the afternoon peak following the school runs, on single decker routes which are busy in the evening rush, are swapped with deckers off school contract runs or swapped with deckers on more rural workings which would otherwise end up at the far end of the route carrying not that many passengers. Also it gives oppertunities to line up the evening wind down so that buses low on fuel which started up early can go to depot or requiring attention can be brought in earlier than planned.
There is also plenty of interworking from route to route and can be changed to give flexibility in times of increased traffic, so that journeys start RT from the City Centre or trips missed out where the cancellation of a run would cause the least disruption to passengers overall.
In the evenings, you generally see branded buses off route or different types used to suit operational requirements. I imagine this is how it works for many other operators. Similar happens on Sundays with reduced frequencies.
To part answer your specific question, Dwell times need to be sufficient to take traffic into account. On a good day, lots of waiting around, on a bad day it runs late, but not as late as it would do without padding.
