If you absolutely must have one FLA only and are only asking how you can save the time of always switching between the publishing options for ios/android then you could write yourself a script with jsfl that automates that task for you.
Sure but why doesn't Adobe, who has been pitching Flash & Adobe AIR as "author once, publish to multiple targets" fix this very simple problem?
I experimented some more and I managed to set up one FLA with two profiles. One is configured for iOS and the other is configured for Android. It WORKS fine except the iOS settings loses all the icons except for the 3 it has in common with the Android side. Conversely, the Android side loses extra Manifest parameters I need for Admob extension integration. It's quite frustrating that this works up to 95% and then loses it. All they really need to do is tie separate app.xml files to seperate publishing profiles.
One way around this would be if I set each profile to publish to a different swf file. AH, but guess what, that is the ONE setting that a profile does NOT save!!!!!!
Thanks for your tip though.