Glad someone has finally explained this to me because I couldn't really find any real information to do with this. If I upgrade I will loose my PCI slot. So I need an external solution for my Universal Audio plug-ins. I sourced a USB UAD DSP effects although willing to look at alternatives as well.
 
So essentially the best way to use Thunderbolt is through a thunderbolt interface or be bottle necked over the USB 3.1 interface. Oh grand.
 

Voda La Void
 
Seems to me any Thunderbolt latency advantage would disappear once converting to usb 3.1.  Am I wrong?  Wouldn't I be restricted to the latency of usb 3.1 then?  

Currently, when it comes to round-trip latency... the best USB-3 audio interfaces aren't out-performing the best
USB-2 audio interfaces.  
ie: The RME Fireface UFX offers 4.3ms total round-trip latency at a 48-sample ASIO buffer size 44.1k.
No current USB-3 audio interface matches this... let alone besting it.  
 
If you're using a Thunderbolt audio interface... with full "PCIe via Thunderbolt" support, you'll see performance equal to using a PCIe card.
 
If you connect a USB audio interface via a Thunderbolt>USB adapter, yes... you'll be subject to the limitations of USB.
 
The best PCIe audio interfaces will allow sub 3ms total round-trip latency.

Tell you what Jim, I'll just ask your opinion before I buy anything....

Think of Thunderbolt as "external PCIe".
 
If your audio interface supports "PCIe via Thunderbolt" under Windows, it will perform on-par with PCIe audio interfaces.
 
Right now, only MOTU and UA currently have "PCIe via Thunderbolt" drivers actually available.
Focusrite is still early in beta-testing.  
If you read the fine print, they currently don't support Thunderbolt-3 connection (which requires a USB-C to Thunderbolt-2 adapter).

There's a lot of hype about Thunderbolt.
If you go that direction... just make sure you know all the details.
If everything isn't in place... it won't work.
 

Far as I can tell and from what I fathomed it's took the place of FireWire in terms of the alternative to usb.

I think if I can get a mobo with all types of port then the issue of having the correct connections will be to a certain extent will be resolved.

Seen an Asus z270 motherboard which has all current standards.

Yeah, I've been reading a bit about them and Thunderbolt's apparent 1 ms latency is very impressive, and makes it seem like the perfect solution for rate and transfer time.   Even the latency of this Firewire set up seems noticeable to me when recording live drums.  This will figure into my next build, coming up in the not-so-near future.  Something tells me this will be my last conventional machine, though, the micro pc's are coming...ha ha 
 
 
 

Check this out!  They claim 32 audio tracks on a $35 brain.  I have this Tracktion Waveform DAW running on Windows.  But it is also cross platform Windows - Mac - Linux, so the same DAW can run on a Raspberyy Pi. 
 
NAMM 2017: Tracktion's Raspberry Pi Based Audio Apps
 

Under ideal circumstances, Thunderbolt performance will equal PCIe.
It will never surpass the performance of PCIe.
 
If super low round-trip latency is paramount, then it makes sense to go PCIe or Thunderbolt (just make sure the audio interface has full "PCIe via Thunderbolt" support for Windows).
Running Firewire protocol via Thunderbolt won't offer any benefit vs running PCIe Firewire.

Jim Roseberry
Under ideal circumstances, Thunderbolt performance will equal PCIe.
It will never surpass the performance of PCIe.
 
If super low round-trip latency is paramount, then it makes sense to go PCIe or Thunderbolt (just make sure the audio interface has full "PCIe via Thunderbolt" support for Windows).
Running Firewire protocol via Thunderbolt won't offer any benefit vs running PCIe Firewire.

Can I still get PCIe Firewire?  I'll Google and see what's out there.  I need to secure a Firewire solution before it all disappears.  I'm not prepared to trade out my Onyx mixer just yet.  But within the next year or so...it will be replaced and I will be looking at Thunderbolt then.  So, I'm just trying to plan for the next 10 years.