When you finish a section on the computer-based PCAT, you can choose to move ahead, or you can wait for the timer to run out if you need a break (or want to use the restroom). You also have the option to take a break in the middle of the test, or you can skip that too.
I took the computer-based PCAT last October and finished in just under 3 hours. I used all the time on my chemistry section and math section, but the others I finished with time to spare and moved ahead.