I didn't know Apple made flagship phones, Apple releases one iPhone model (or two sizes) every year. There is only one phone - flagship or not, it's cost is what it has always been and not comparable to other phones because of factors other than just the hardware. One factor is the OS, the cost of the iPhone includes the cost of OS, while the free Android OS is free because the user data has a monetary value to Google and the ad industry. The value of user data to the Google/ad industry and value of the data in the eyes of the user are two different valuations. Android phone OEMs don't have the cost of developing their own OS or ecosystem or app store etc., so the assumption from the getgo should be that comparable Android phones have to be cheaper than an iPhone. Even the so called superior hardware phones should be cheaper than an iPhone.
Just the cost of the hardware is just one part of the price of the device, it easy to focus on the cost of the hardware because that it is readily estimated, but the cost of intangibles like OS, hardware software integration, ecosystem, backbone/infrastructure (eg. services like Facetime, iMessage, iTunes) customer service are not well defined. It's naive bordering on imbecilic to think that one company could take the hardware inside an iPhone and make a comparable phone or be sucessful. Or think that iPhone is too expensive. I think iPhone is fairly priced when you compare the price of GS6 etc. is the similar to the iPhone.
And what's astounding is that Android OEMs are not able to thrive under the Google's free OS plus the ecosystem model while Apple can thrive when Apple does everything that the Google/Android collective does.