A few points:
"The form factor is already there".....Well no it is not, there is a larger pentaprism that causes the bump, one of the really nice features, a Dx camera with a big bright VF that would not allow a popup flash also unless increasing the size of the body. Better VF trumps puny pop up flash any day
"CLS uses the IR port", actually it does not use it any more than non-CLS, CLS works with a series or call and reply light pulses that occur so close in time to the exposure flash that we don't notice them. When I was designing a RF controller back in 2008 when the D90 came out, I set up a phototransistor detector and measured the pulses for timing, pulse position in the pulse train and duration so I could duplicate the control system with RF instead of with light. It is a complex series of pulses the triggers each group independently and measures the return from the subject using the regular metering sensor, not the IR port which would not have the sensitivity or DR to be practical. After triggering each group separately another pulse train is sent coded for each group with power calculated values. And finally the pulse that triggers the remote flashes to fire in the power setting just previously sent. This all happens before the shutter opens which allows the exposure command flash to not contribute to the exposure if you set the onboard flash for that. I was able to build a RF system that worked great without the flash on the camera raised at all. Pocket Wizard did something similar 3 years later so I guess I was the first to create an RF system.
If someone needs controlled light on a subject they really need to control the beam in more ways than the fixed position of the popup, making the popup only useful for close in snap shots, without a lens hood(which casts wide shadows on the bottom of the frame) which makes it pretty useless for any serious shot. A better alternative is just use your smart phone for those very casual snap shots, they are perfect for that. You do not spend $5k on a body and pro lens for snap shots that are easier done with a smart phone. A D3300 is a much better use of the money, with kit lens for casual snap shots. Everyone who is not shooting action sports in burst mode finds as their camera level increases their shot count drops, due to a number of factors, but one of them is more time and more deliberate planning goes into more serious shots so a landscaper might come home with less than a dozen where when they started out with a D3000 or D5000, they probably were shooting 300 shots in the same setting. The files were small, the effort to get the shot low, and hope was more a factor that was not when they became more masters of their equipment so shots were less luck and a lot more intentional results.
A D500 might be a great snap shot camera but why? The same images can be had for a great deal less money for casual snap shots. The difference is when you graduate to wanting more detailed control of the shot. That is why experienced shooters almost never have need for a popup flash, it is one unused item gone that took valuable space where a larger pentaprism should go, and 1 less thing to break accidentally.
Flash and creative use of it has more impact on image quality and story telling ability than any camera body can have. Light, and shadow is all the photographer has to create with, it is his paint brushes and oils, so if one is limited in funds, like every one of us is to various degrees, the absolute best place to use those funds is lighting and learning to use it, and not camera bodies which have a surprisingly low importance in determining the quality of an image or its ability to tell a compelling story. By the time someone moves to a D810 or D500, lets hope they needed it only after having the lighting skills already well developed or else they wasted good money. Yes, a D500 is a GREAT camera...but so what...it is 10% of an image. A D3300 and good use of light, and shadow to tell a story will beat out a D810/D4 every single time without deliberate control or use of the light and shadows. The rush to high ISO undermines creative use of shadows I find but that is the popular trend. Portraiture of the 30s and 40s when ISO was 24 or 64 was the era of the great portrait photography and why those images are still found in gallery walls today, they certainly were not hampered by poor light sensitivity. Even action sports has little improved images over 40 years ago.