Someone has already pointed this out but R&D costs are a fixed cost overhead which has already been spent and factored into the companies budget/finances. So if anything the higher price point tells me that Microsoft is not expecting to sell large volumes of these devices, they are keepoing people happy by releasing a flagship but at the same time trying to extract as much profit as they can out of each individual device. I also don't think they are too concerned about recouping the R&D costs, Microsoft would be spending billions on many different R&D projects each year that never see the light of day. So what is their tactic? Who knows
As an example of the cost benefits to Microsoft, lets say the cost of the parts in these devices are somewhere around $230.00 which is apparently similar to the iPhone 6S, add a further $20.00 to offset Apples volume purchasing discounts on the parts, add a further $15 for manufacturing costs (assembly and testing) and a further $5.00 for shipping and you have a cost base of approx. $270 per device to get the devices into retailers hands.
If Microsoft has already spent $200 million on R&D to develop these devices and would spend a further $200 million on marketing them, it would only cost them $400 million in total in fixed overhead costs. So, how many devices and at what margins does Microsoft need to obtain to recoup these costs and turn a profit. If they can sell 5 million units per quarter over a year, which looks to be achievable based on previous WP sales volumes, they would sell a total of around 20 million units in a year. So to break even they would only need to sell these devices for around $290.00 each.
Why don't they sell them for $325.00 with a RRP of around between $375 and $425? This would generate $35.00 profit per device or $700 million over a 12 month period. This $700 million could be kept as profit or could be channelled back into additional marketing or bundling accessories and services and further driving sales and market share.
The only reason I can think for the higher price is due to the fact that they do not want to discourage other OEM's from creating Windows 10 mobile devices, but who would they be discouraging? The only OEM's that would have any impact on significant sales volumes would be the big players such as HTC, Samsung, Sony, the problem is that none of them so far have committed to build any high end Windows 10 devices. Secondly i don't think they would be worried about Microsoft releasing a high end low cost handset, the Nexus handsets haven't stopped them, either has the OnePlus One handsets. These big OEM's will make handsets for whatever platform they see as viable and can produce a profit for them and until the Windows 10 market share grows this is not going to happen.
At the end of the day these handsets at these prices will not compete with iPhone or any similarly priced Android devices. The only people buying them will be the Microsoft fans that already have a Windows Phone. The result being that the market share will only reduce or at best stay the same as it current is.