That $50 savings isn't a perception only relevant to the 64GB Nexus, though. It's also relevant to the competing, better known brands, against whom that savings helps marketing position. No question that offering a single model would reduce its cost in comparison to the same model as one of multiple variations, though. I suspect that if they had offered only a single memory size, carriers would have exerted what pressure on Google they could to have it be the 32GB size, since the vast majority of consumers who would want the Nexus 6, who are coming from phones with similar or lower storage, would not think it a deficit.
As to on-contract pricing, bear in mind that there has been some movement in the industry away from carrier subsidies, and even carriers that distribute the cost of the device to the consumer over time still make it quite clear that they will receive the full retail of the device when all is said and done.
Nexus isn't the product that nobody's heard of anymore, and by pushing the envelope in size and finally with a truly premium device it's garnered some interest, but it will take at least one more cycle of evolution and substantial marketing push (the scope of which could hardly ever be expected to match the level of market development funds provided by an OEM for any OEM-driven phone).
I'm just hoping Google gets over the notion of the cloud being as widely continuously available and supporting bandwidth needed to alleviate the need for on-device storage, which has the potential to grow greatly if technologies like 4k video gain any traction. Allowing for removable storage in future Nexus would go a long ways towards negating the need for multiple RAM models, though DRM is still understandably a concern.