Shouldn't Microsoft have the right to dictate at least the initial end-user configuration of their products?

Either the OEM's are buying Windows or the end users are. Since Microsoft got a whole set of lawsuits dismissed on the grounds that the end users weren't the actual purchasers of their product, and thus had no standing to file a lawsuit, Microsoft has obviously taken the position that the OEM's are their customers. Once the OEM's have taken delivery of the product, they are free to modify it's specific configuration as much as an end user.