JRemote is primarily a remote control. When it is being used in "normal" remote control mode, it is just sending commands to MC. MC is doing all of the playback decoding and processing. JRemote just shows you the album covers, song titles, etc, and sends commands to MC based on your input (touching the screen).
However, JRemote has a "this device" mode, which sends the files from MC *to* JRemote. The JRemote device then plays back the songs using it's decoding. I believe this is usually done by transcoding the original files in MC to MP3, then sending them to JRemote, and then JRemote decodes the MP3s. I'm not 100% sure about this last part.
But I *am* sure that JRemote has a "this device" mode. It's usually used so you can listen on headphones plugged in to the JR device, or to play back from the device to bluetooth speakers or something. I believe there is a wheel or cog control in the lower left hand part of the JRemote interface which allows you to choose your sound source: From MC's sources, or to "this device".
I'm not away of any way for JRemote to send "phone sounds" to MC. I would think the only way this would happen is if you were using JRemote in "this device" mode and then sending the audio to your receiver via bluetooth or perhaps Airplay and that the i-device was also sending it's notifications there since it would be the default audio target.
Brian.