I've got to agree with Wims here.
"Pause" by its very definition means to save the state of something as it is at that exact moment so that you can resume it later on. If you pause a timer with 3 seconds left until it triggers and resume it later, it is logical to expect that the timer will take 3 seconds from that point, otherwise the timer does not pause and is still ticking after running the pause command.
That said, this has the potential to break scripts so it would perhaps be better to implement true pausing using another method. Maybe -p/-p0 can still trigger the current method and -p1 for Wims' expectations.
