I noticed a different when creating an .ipa file manually using
/usr/bin/xcrun -sdk iphoneos PackageApplication -v "DerivedData/MyApp/Build/Products/Release-iphoneos/MyApp.app" -o "~/MyApp.ipa" --sign "<HIDDEN>" --embed "<HIDDEN>"
I'll answer myself -
In Xcode 7 Apple added the ability to specify export options plist file to better control the .ipa file creation.
One of the options there is
<key>uploadSymbols</key> that does exactly what I need.