This has been reported before:
https://forums.mirc.com/ubbthreads.php/topics/230738/pausing_timer#Post230738and you had already +1'ed the backwards-compatible requested fix:
https://forums.mirc.com/ubbthreads.php/ubb/showflat/Number/230920-p1 would offer the documented behavior instead of the backwards-compatible behavior. Currently, instead of pausing the timer, the .secs countdown continues to zero, and only then does it pause. There's effectively no difference as to when you use -p as long as you do it before the next .reps execution.
The documented behavior is misleading. If this were an mp3 player, when you paused the player it would continue silently playing the song. If you resumed the player before the song ended, it would resume as if you had temporarily turned the volumen down. But if you resumed after the time when the song would have otherwise ended, it would begin the next song instead of resuming play of the portion of the song you missed.
This shows the countdown continues to zero while it is "paused":
//timerx1 2 7 noop | timerx2 10 1 echo -a $!timer(x1).reps $!timer(x1).secs | timerx3 1 2 timerx1 -p
