I'd expect the base file to contain my English words since my project has "Localization native development region" set to English.
Update - to clarify my question:
Apart from addressing question what language end-users will see, you need to consider also what will be shown in the AppStore. My current experience is that if you use Base for English, English won't appear in list of supported languages (how Apple knows in which language your base localization is) in the description of your app.
I've met this issue myself - base (English), German and Russian
Target settings refer to:
Localization native development region = en
But on Appstore it appears in this form:
Languages: German, Russian
no reference to English
I consider to duplicate base localization to English (not a high priority, as users see from screenshots that App works in English anyway)
Edit: there seem to be a different behavior in iOS8 - Application Settings (Settings.bundle) seem to ignore Base translation, if any of translations match your "Preferred Language Order".
In other words, App is localized: Base, German, Russian. iPhone is configured to use English, preferred languages order is English, German, Russian.
Application settings come in ... German!
Once again: this is applied to Settings only not to the application itself!