I had been using Xcode 4.2 up till last week and I was using the size of my .ipa file to estimate the size of my app in the app store (I've kept it just under 20MB) and its been pretty consistent. I upgraded to Xcode 4.3 2 days ago and it has a new feature to indicate to you the 'Estimated App Store Size' after you 'Archive' your app, the estimated size its giving me is fully 2x the size of my .ipa file I've been using to guess my app store size and its WAY over 20MB according to Xcode 4.3!
So, which one is right? :O
EDIT: Just released the app today and it looks like the ipa was the closest guess in my case the app shows in the store as 17.6MB and the .ipa is (now) 16.7MB, 3.3MB binary.
You can more or less ignore XCode's "estimate" (or roughly cut it in half) for most iOS apps. The IPA is the size of the app. This doubling in estimated size seems to be linked to the architecture build overhaul in 4.3.2. Since you are likely building your app for "armv6 armv7", it's doubling it for some reason. I recently uploaded my previously 15MB app with minor changes. XCode shows 30MB estimated size for the archive. Sure enough, the new app is actually 15.2MB on the app store.
If you want a better estimate, simply right-click the archive in the Organizer and select Show in Finder. There, you can again right-click and drill down into the archive to see the actual package and contents. The app is the only thing of substantive size and is a very good estimation of the App Store size.