Keith,
>>So was this the result of less code from the stripped swf assets being inserted into the main swf file?
Yes. In AIR 3.6 with multiple swfs feature on iOS we started embedding all ABC code of the secondary SWFs into the main/root SWF (as for iOS we can load only compiled code) and all the secondary SWFs go as stripped SWFs in the IPA.
I hope it clears all the doubts!
-Nimisha