I see that the motherboard (E178, Z170 Classified K) comes with a thunderbolt GPIO. 
 
I have purchased a ThunerBoltEX 3 PCIe card (Asus) and installed it into PE4 (uses 4X Gen 3 connection from PCH). I have the thunderbolt intel option turned ON and pointing to that PE4 slot in the BIOS. Note: this card states it is capable of 40Gbps via the type-C port, and SS10 (10Gbps) via the Type-A port. The Type-A port works fine, but I do not see the Type-C cable working with anything I plug into it. (I am using a Type-C to micro-B cable to test if I can attach and power slim 2.5inch HDDs) 
 
I have NOT tried a Type-C to Type-C cable. 
 
My question is: can this Asus ThunderBoltEX 3 card work with this motherboard? I see the ThunderBolt intel base on the BIOS states it is Falcon Ridge (Thunderbolt 2?). Do I need to plug in the 6-pin power connector at the bottom of the mobo so that each PCIe lane has it's own power (and thus, power can be received via the type-c port to spin-up drives)?

"Do I need to plug in the 6-pin power connector at the bottom of the mobo so that each PCIe lane"
You need only connect this if you are using 3 or More Graphics Cards.
Myself I use it if even only 1 Card. It relives the Power taken from the 24-Pin Power Cable.
I have 4 Graphics Cards and this 6-Pin PCIe Connector Pulls 130-150 Watts.
 
"can this Asus ThunderBoltEX 3 card work with this motherboard?" Test it and let us know!

 
From "Anandtech by Anand Lal Shimpi on June 9, 2013 8:39 PM EST "
Falcon Ridge however is designed to address this problem later this year. Falcon Ridge will officially be the first controller to implement Thunderbolt 2. Despite the increment in nomenclature, the differences are actually pretty simple.
Today, Thunderbolt exists as four 10Gbps channels - two upstream and two downstream. Each channel however is fully independent. Although PCIe and DisplayPort are muxed from the cable perspective, you can only send one or the other over each channel. That limits max performance for a single storage device to 10Gbps (minus overhead), and it similarly limits the max display bandwidth to 10Gbps as well. The latter is insufficient for 4K video (~15Gbps depending on refresh rate). If you bypass Thunderbolt and just send DP 1.2 over the cable it's not a problem, but if you want to enable mixed use cases where you're driving both 4K video and high-speed storage over the same cable you're going to need another solution.