Fair enough. Unfortunately price comparisons are not of any use in this scenario.
Macs are not Windows machines.
Windows machines are not Macs.
For equivalent hardware you will generally spend more money on your Mac than you would in a Windows machine. You can argue engineering, software, support, what have you. It really does not change the fact that in most circumstances, based on hardware alone, Macs are more expensive.
So the mini, which really has no equivalent in the PC world, has a notebook hard drive. In order to keep costs lower and profit margins up Apple cut a couple corners. Either accept it or don't.