Lumping the development costs with the price of the manufacturing
IS the only way to do the accounting for the cost of the console and there is NOTHING disingenuous about doing so. While it is true that their business model is up to them, the ability to use your hardware as you see fit is quite another issue.
Now, what might be acceptable is for Sony to say if you use your PS3 for a Linux console, you can only use it for a Linux console, not both a Linux console and a PS3. But I do rather think that any system bought under the original license which said you could do both ought to continue being able to do both, and Sony ought NOT be able to change the license just by updating the firmware*. The concept of a contract has always implied some negotiations between both parties. Absent negotiations, there tend to be laws limiting the sorts of changes one unilaterally can make to the contract.
*This might be a licensing and tracking nightmare for Sony, but that's their problem, not their customers. Like selling a console below cost, it's part of the business model if they choose to undertake it.