We have two choices for the main motherboard:
♦ High spec "Z-series" Skylake motherboard with USB3.1
♦ Standard "H series" Skylake motherboard
The two boards are very similar. The biggest difference is that the High spec board has USB3.1 on board where as the normal board has USB3 only. USB 3 is the standard we have been using for the last few years and is very fast. USB3.1 is a new standard which is considerably faster with the right hardware. Currently no hardware is available to take advantage of this, however, there will undoubtedly be many becoming available of the next few months. Therefore, if you want a more "future proof" system is makes sense to get the motherboard with USB3.1 for not a great deal of extra money.
The Thunderbolt add-on board
The High spec motherboard can have a Thunderbolt board added to it so that you can take advantage of Thunderbolt devices. Thunderbolt has been around for some time and there are many Thunderbolt devices available. It is used more on MACS where there is no way to add any devices inside current Macs and Mac Pros, so they have to be added externally via Thunderbolt. On a PC there is generally an internal PCIe device which can do the same job as an external Thunderbolt device so Thunderbolt is not essential on a PC.
The Thunderbolt add-on board for the Skylake systems has not yet been released but there will be one in the next few months. Because the Skylake systems have limited resources compared to the Broadwell or Xeon systems, if you add the Thunderbolt board you will have to loose something else - for example, you probably cannot have a Blackmagic Intensity Pro 4K in the same system as a Thunderbolt board.
The ability to possibly add a Thunderbolt board sometime in the future is nice, but not essential, but it is another thing which is different between the High spec and standard motherboard.
We have chose the High spec motherboard as the default board in this system because we believe that most people will choose this option, given the small price difference. Obviously it does not quite make sense that the "standard" motherboard is not the default one, but we did not want to call it "low spec motherboard" as that would give the wrong impression. The standard motherboard is very good. The high spec motherboard is better and not much more money.