One issue with surround sound on Sky is the two or three seconds of silence as it switches between 2.0 and 5.1 and back again, and the blips that cause similar silences part way through programmes.
I believe the problem varies a lot depending on the AV equipment, but isn't possible to get rid of entirely.
That's not a Sky issue, it's down to how the receiving equipment handles the format change.
I don't have an AV receiver so I'm listening in stereo through the TV, but my Sky Q box is set to feed Dolby 5.1 so my TV still has to handle the format switch between stereo audio and mixed down Dolby audio. All that happens on my end is it mutes for a very brief period (less than half a second), other than that you barely notice it changed.