Certainly they can be separated to a point. But, are they. I'm betting Amazon and the others, at some point, take into the consideration all of the outlay before factoring in required profit. There may be a certain separation of costs but, when the corporate bottom line is examined, all the attendant costs must be considered. All the expenses required to bring an e-pub to market must be considered, reader development and production, scanning, proofing, all of the overhead including salaries, rent etc. and then profit is added in.
I'm guessing each step must stand on it's own and be contributing to the company's fiscal health. This is particularly important for a publicly traded company. But, the e-reader was developed to provide a market for the publications and there is where the profits will be realized. One can bring down the cost of the reader by purchasing one with ads and only WiFi capability. The costs of publishing before factoring in required profit are probably fairly static, but the need to provide newer/better readers must be factored into the publications retail price. Retailing the books is where the profit is most easily realized, not the readers, I suspect.
I'm talking through my ass here as I'm not directly involved in the process. I may be entirely off base but, I see the economic logic in my argument. Nothing Amazon and the others providers do is altruistic or based on improving the world. Not even their various donations to non-profits. For the companies it's all driven by profit motive and growth. The owners/founders, once no longer dependent on the company, are then free to do with their moneys, not the company's, as they feel so moved.