To clarify what iOS uses to determine "version" versus "build number" it is the iOS Info.plist values for CFBundleShortVersionString and CFBundleVersion respectively.
AIR has two app descriptor elements, versionLabel (which maps to CFBundleShortVersionString - iOS version) and versionNumber (which maps to CFBundleVersion - iOS build number)
AIR also has a "feature" where if you only specify versionNumber in your app xml, it will use this same value for versionLabel too.
So I think you are technically using the same value for version and build number if only using versionNumber.
If you are currently using something like:
<versionNumber>2.0.3</versionNumber>
you might be able to just switch to something like:
<versionLabel>2.0.3</versionLabel>
<versionNumber>100</versionNumber>
(where 100 is 'higher' than 2.0.3)
and then going forward bump only your versionNumber for new builds and only bump versionLabel with updated public releases that also affect Apple's version changes for the store.