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That's not allowed, but you can charge more for the native app version and give it more features. Charge $6 for the native app, but add offline reading. Charge $4 for the web version.

Nope. Apple's terms are explicit that iTunes price has to be lowest possible option (though others can be equally low). They've offered publishers like Conde Nast a tiny bit of wiggle room, by allowing them to sell print + digital bundles on their own sites; those bundles are more expensive than the all-digital subscription offered on itunes, but you could argue that they effectively discount the digital portion.

No. One of Apple's terms is that you must offer the same price.

This is not permitted.