Yes. I experienced this same issue with HDMI to my television, and optical digital to my old receiver. In my experience it has always been the HDMI connection between the Oppo and the TV that results in the prolonged handshake/audio muting. If I disconnect the HDMI to the TV, the audio muting does not occur.
The benefit of 1080p24 is to have each of the 24 frames per second (from film sourced Blu-ray discs) shown at exactly 1/24 second intervals, assuming your TV supports 1080p24. At 60hz (1080p24 turned off), some of the frames have to be shown longer than others since 60 isn't evenly divisible by 24. Some people notice the resulting motion judder more than others.