Agreed on the convenience point. FT's strategy is definitely dependent upon the consumer's loyalty to their brand/product. Enough that they'd rather see Apple's cut stay with the publisher at the inconvenience cost of dealing with separate bills.
I'm not sure about the terms of Apple's in-app purchasing (perhaps someone could elaborate), but can a publisher add a surcharge to the native app, to cover apple's cut, then offer the original (now discounted) price to users who pay through the web app or via a webpage?
This is not permitted.
No. One of Apple's terms is that you must offer the same price.
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.