For example: COnfiguration of the system. OSx's simplistic "preferences tab" beats the snot out of Windows Control panel, which is often "too much". And Linux.. well... I have hard time ever recommending linux to a non geek (Though I like it for its uses too). But, on the flip side, the sheer openess of windows makes for some intresting configuration and customizability options unavailable in OSx.
OS X is quite customisable - many parts of it use a plugin-based architecture, its kernel and much of the low-level stuff is open source and it includes a unified configuration framework (defaults). Don't be fooled by the simplicity of the Preferences - the system has much much much more options under the hood. And if you want customisability: out of box it includes things like Automator and I don't even want to start with the amount of customisability you can do with Launchd daemons.
You could just as easily use a dual SSD PCie card with enterprise SSDs. There's plenty of existing solutions like that for the older Mac Pro that offers equal or better Mbytes/s than the PCIe SSDs the 2013 Mac Pro comes with.
I know you want exact, like for like but that doesn't mean there isn't alternatives that offer the same speed benefits and in either case, you're paying a lot for a small PCIe SSD blade instead of a larger equivalent PCIe card.
I am simply saying that I want to see equivalent components. Its not hard to build a cheaper machine by using parts which are inherently cheaper. In our case, we are taking about almost 2x performance difference between the consumer SATA-based and enterprise PCI-e based SSDs. I am not talking about a SSD blade either. And BTW, a equivalent PCIe card is usually much more expensive that what Apple charges. For example look at this 800Gb SSD from Intel: http://www.newegg.com/Product/Product.aspx?Item=N82E16820167126