They weren't that far off in terms of the Nexus 6 vs Note 4 last year (Nexus 6 32GB was $649, Note 4 32GB was $700). This year Samsung upped the price of their Note series significantly, getting $700 for the 32GB vs the 6p getting $550 for their 32GB model. But even before this year's or the Nexus 4 & 5, the Nexus 1 and and Samsung's Nexus S and Galaxy Nexus were getting as least as much as their rivals. While recent models may not have had as much profit as the early devices, which also has to do with the OEM since LG, Asus, and Huawei have all been able to offer their own devices at an affordable price point, they're not selling them for $10 above cost (except maybe for the 5x).
Nexus 6 mark up was still below average. Then add to a device that has low demand. Leaving the profit per device compared to the Note 4 below average. If nexus 6 was in high demand could made similar profit per Note 4.
Nexus 4,5 both based on lg devices that were marked up respectfully. Where the Nexus counter parts with more hardware or curved glass which would increase cost that similar device also had mark up cut below average. Basically Nexus were selling LG G1 and G2 at lower cost and less of return due to low demand. Build cost similar to G1 and G2 the nexus 4 and nexus 5 but mark up below average and demand below average, Then add particular design choices in Nexus 4 and Nexus 5 that could be mass produce part they took from higher demand G1 and G2 just adds to the below average profit.
Nexus S and Galaxy S different oem then lg but same problems.
Nexus 1 was a one off and 1st gen to may device HTC would make after. I believe mark up cold have been average. Since HTC Nexus One was first it kind it's build cost probably higher than average and nexus one had low demand.(Particular because how it was sold) That profit nexus one was below average as well probably alot worse nexus devices in general.
May I ask where you're getting that they're using older hardware? All of the components, except for the display since I don't know where they sourced it from, are the same components used in other devices out this year. The camera is an updated unit from last year's Droid Turbo, the 808 is used in many current models (usually in lieu of the 810 due to its tendency to overheat), the RAM is the same as many others are using (except for Samsung who switched to DDR 4, which is probably one of the reasons they are selling at a higher price point). But while it may not be bleeding edge, the fact that they have offered what most other competitors are but at $100-200 less should say something. And since they're not going to sell them at a loss, that means that other companies are padding their profit even more than they have to.
Your talking about MXP right. You just answer your own question. They using 808 which older than 810. MXP uses a lot mass produce parts from other models like camera. The camera camera cam from a Droid turbo(Turbo release OCT 2014), The MXP is using older or mass produce devices that parts to make the device makes the device cheaper per unit to a N6P. IF MXP make profit is not reflection N6P because build cost,demand, and mark up are not same.
There's two ways to look at it, sell some devices at a high profit, or sell more models at a lower profit. The former looks very good to board members and investors, while the latter gets you more customers. And if you don't screw it up, they will be return customers. Once people (at least in the US anyway) start seeing how much they're actually paying for their devices (something that wasn't as clear with phone subsidies in place, I'd imagine they'll look to devices that can still fulfill their needs, but at a lower price point. I imagine that OEMs have known that the end of subsidies were coming and that's why you're seeing these low prices flagships start to show up more visibly, because not everyone is going to want to shell out $700+ for highend devices going forward, especially if we're looking at another recession in the near future like some are predicting.
This whole different separate and start of different topic of debate. This idea your talking about is overall look at mobile industry through the perspective of selling unlocked off contract devices that Moto has been doing since the launch of the Moto X. That MXP is flagship device with the performance close that to high end devices but at cheaper cost. Which in long run the mass will prefer low cost unlocked flagship device rather than buy the subside high end device or highend unlocked $700 device. Furthermore when mass change then more OEMs will in employ strategy Moto is doing with the Moto X line. Well if Moto is successful I could see a shift how mobile industry prices and sell devices in future.