Note: This has to do with App Slicing and App Thinning that was introduced by Apple in late 2015. Nothing to do with your 2012 question.
http://www.imore.com/app-thinning-ios-9-explained
http://www.macrumors.com/2015/10/05/ios-9-app-slicing-now-available/
http://www.appcoda.com/app-thinning/
Given that my iOS storage has been running out of space, I try to keep iOS App versions which are smaller in size and not update unless essential or compelled to {e.g. Uber compels updates}
So, I recently did a comparative analysis for 2 apps and what sizes (in MB) they show in 3 places (iTunes 12.3.3 On Windows 8.1 x 64):
App Names:
Todoist 11.0.3
Wunderlist 3.4.3
Current Latest Versions updated & synced this weekend:
iTunes > AppStore | As shown on AppStore before download
70
95
iTunes > My Apps | As shown in iTunes after download
34
53
iPad 2 - iOS 9.0.2 > | As seen under iTunes > Sync > App Selection area after Install/ Sync
65
87
iPhone 5 - iOS 9.0.2 > | As seen under iTunes > Sync > App Selection area after Install/ Sync
XX
YY
{Will post these numbers soon as well}
I cannot understand why the "complete un-thinned App from the AppStore would take more space when thinned for the iPad or iPhone"