The original article states that the Windows machine is without any Thunderbolt 2 connectivity. If you wanted to match the hardware more closely, you would have

The original article states that the Windows machine is without any Thunderbolt 2 connectivity. If you wanted to match the hardware more closely, you would have to add the price of fairly expensive Thunderbolt 2 add-on cards. I'm not even sure you could match the 6x Thunderbolt 2 ports and 4x USB 3 ports available on the Mac Pro with a DIY PC at this time. The Mac Pro also has dual gigabit ethernet and built-in speaker, which this comparison does not seem to take into account.