I think one of the issues we're running into in this discussion is the definition of what a flagship phone is.
In 2017, here's my definition:
It must have the latest available processor, maximum usable RAM, a minimum of 64 gigs of mass storage and a fingerprint or iris scanner. And it must also have superior build quality and long battery life. After that, everything else is a feature that some people will want and others won't care about one way or the other. Features will determine for an individual whether or not it's the smartphone for them. That's why we end up with differing opinions about what is currently the best (in this case Windows phone). But the lack of certain features should not disqualify a phone from being considered a flagship.
Let's start with the camera. I came close to adding a high quality camera to my must haves. But then I considered how many people that have a smart phone that rarely or never take pics or video with it. Then there are others that take pics daily. These two groups of people would view the camera differently.
NFC: I never use it and likely never will IF it continues in it's current state of implementation. For the purposes of making payments, too many retailers are not on board. I'd rather consistently use the same method for making payments, which is why I continue to use a credit card. Pulling out a credit card is no more of a hassle than pulling out the phone. For the other uses of NFC, it's too inconsistent. That, said, there are people that use it regularly for making payments, so for them it's a usable feature (frankly, even though I know that, I've never seen anyone paying with their phone, so it makes me wonder what percentage of transactions are completed this way?).
Wireless charging: I've never had it, so I don't miss it. It's takes me a matter of seconds to connect the USB C cable. But others find it to be a great convenience.
Glance: I had it since my Nokia N8 (which I still use as a bedside clock) so I understand the convenience. But, I really haven't missed it. It would be a welcome addition, but it's certainly not a necessity.
Continuum: For me it's a major selling point and something I use regularly that takes the phone to another level of functionality. But for others it's a feature they'll never use (and if it was a requirement for a flagship, no other OS would have a flagship phone!).
I could go on, but I think my point is clear. Sometimes we just get it in our heads that we "need" certain features, probably because we like to see a phone loaded with specs. For a long time I would check to make sure that the phone had FM radio when I was looking to make a new purchase, until I realized it's a feature I haven't used in a very long time (and if I suddenly get the urge, I still have four phone what have FM). What I'm saying is, For me the Idol 4S is the best current Windows smart phone, even with the shortcomings of the camera. But I can understand that the camera alone could be a deal killer for someone else. But just because a certain feature is a deal killer for me, doesn't mean a particular phone does not deserve flagship status. Even with the few things that this device doesn't excel at (or doesn't have), I believe it's a worthy competitor to any flagship regardless of OS.