It seems far to easy to get the editor out-of-sync with a given player build platform. We should prevent the user from building in this situation. To reproduce this bug:

1. Install Unity version 5.3.1f1
2. Install the Unity Editor only, version 5.3.1p1 (I used this link: http://beta.unity3d.com/download/7d3d8e90548b/MacEditorInstaller/Unity-5.3.1p1.pkg from the normal QA patch releases page: http://unity3d.com/unity/qa/patch-releases)
3. Build an empty for iOS (which _seems_ to work fine)
4. Open the generated Xcode project and attempt to build it. I see lots of errors like this:

Bulk_Generics_0.cpp:256:3: Use of undeclared identifier 'il2cpp_codegen_initialize_method'

These errors occur because the iOS player build is from version 5.3.1f1, which won't work with the code il2cpp.exe generates at version 5.3.1p1.

More generally, the Editor should probably detect this version mismatch and prevent the user from building.