No, it's not about $50 more, it's much more. Be accurate, be exact please.
How Apple treats all taxes is really irrelevant, the the final price that the customer pays is what's important here. The price customers pay when they leave the Apple shop.
Just in those sample countries, the customer at the checkout pays:
Great Britain - $137.86 USD extra
Australia - $123.78 USD extra
Japan - $70.19 USD extra
iPhone 6s Silver 16GB
USA - $649.00 = $649.00 USD
Great Britain - £449 (£539.00 - VAT £90.00) = $655.36 USD or $786.86 USD including VAT which is what the customer pays
Australia - $980 ($1,079.00 - $99) = $701.88 USD or $772.78 USD including GST which is what the customer pays
Japan - ¥78,800 = $719.19 USD
Further, according to Apple's site, iPhone's in the above sample countries come with an Apple One (1) Year Limited Warranty. Any other additional guarantees a country might offer as protection from defective devices is up to that country, it has nothing to do with the price customers pay when they leave the Apple shop.