You have 45 seconds to return to your pop up and return. If it is a quick potty break shouldn't take 2 mins.
I would suggest to you if you're not going off too far, when you're away/tab from game, go to options
and let system sounds on so you can hear. Saved my life so much.
Having them auto accept is a bad idea, since you'll be AFK in the dungeon too.
Pausing only backs up the line for other DPS ready but waiting.
Just take your breaks as soon as you Queue up or before like MetalWrath said.