One way of working with comping midi is to hit Ctrl-L after comping the selected midi data area. This will prevent the midi clip from looping. A pop up window will show this; just click ok.
Comping of midi tracks will also allow splitting of the track so that you move it, edit it duplicate it etc...
As Beepster mentioned, after all is done simple bounce to clip to get a single continuous clip.
The only weirdness i am experiencing is related to refresh and display problems. Sometimes after any edits, including comping or other edits, the midi notes disappear from the screen. They are still there but not seen after the edits are done. Opening the PRV will still show the notes and sometimes, shifting to different areas of the track view and coming back, the notes either show up or not...