This will be a popular topic!
I've also run several tests with CocoonJS and AppMobi too, but in Android.
CocoonJS launcher(version before the update in 2012.09.12.):
The BG Music plays well, but it used to not loop, so I need to make a hack for it (stop+start BG music in every several minutes).
The audio plays well, but in my specific app, what plays 15-30sec narrarions as audio the narrations play for about 10sec and stop.
I used to have a fix for audio play lenght - C2 preload sound - but it only worked with on of the prev. versions of the launcher... :(
AppMobi Test anywhere (C2 Browser export) + AppMobi new C2 plugin:
The work in progress new plugin is accessable here: scirra.com/forum/plugin-appmobi-plugin-updates_topic55572.html
For this to work I need to use the AppMobi's new plugin's own Audio actions, not the C2's default audio actions.
BG Music OK, no looping, but I used the same hack like with Cocoon.
The narration: used to be OK, than the plugin have file name Upper/Lower case bug. It may be fixed already...
My biggest problem about AppMobi, that I need to use specific Audio actions to get working audio in the Android. Additionally the AppMobi XDK never worked the same way as my builded app especially with audio objects.
I did not noticed any difference between the 2 build ways.
All the 2 builds gave me great FPS, and not noticable delays in opening new pages, menues, etc.
I noticed that the AppMobi seems to downloading the contents of the app when it is first started. This is a hell for a multimedia rich app - like my book with 76 pages + 76 narrations. :(
The CocoonJS launcher (not the very last version) used to freeze sometimes when I use preload music. Without it, it were very stable.
Currenctly the AppMobi XDK can not be loaded in my PC, but works well in my Laptop. This is something related to Java, but ohhh... I can not fix it in 5-6 hours, so gave up.
The builded app seems to be stable, did not freezed anytime.