Yes, if you need to silence a track and bring it back later still in sync with everything else, use Mute.
Pause was always kind of a half-finished thing. Unless you're using it for effect with non-rhythmic content it requires scripts with wait statements to time it. One of the things I've been working toward with external quantize in b46 is making it more usable by allowing Unpause to be quantized to other things.
As @steg_music mentions, Realign can also be used but it isn't automatic, you first have to Unpause and then do a Realign which again requires scripts to avoid a little sound blip between the two. That's another thing I've been working on, various forms of auto-realign that would be good for several things. Besides Unpause, switching between loops, when one of them is empty has similar alignment problems.