the current behaviour is, in effect, the sum of what it ought to be plus a potential single execution of /timer -e. if it were changed to behave in the way that it ought to behave, a user could replicate previous behaviour with /timer -r followed by optional /timer -e depending on the result of a calculation involving $timer().secs before and after the pause. however, as it stands, it isn't nearly so simple to script /timer -p that functions as Wims believes it should, and as is suggested by the phrasing 'pause a timer'.
That wouldn't work because /timer -e does not reset the time before the next execution. Therefore changing the behavior as you suggested would require you to use $timer().secs to reproduce the original behavior, so you're really just swapping the two behaviors in terms of how difficult they would be to implement.
That's why I thought both behaviors could be added natively. /timer -p could be the current behavior, and a new switch could implement the behavior Wims is asking for.