I'm aware of how Thunderbolt eats PCIe lanes. I don't need it nor think I will ever use it, and worse if I consider that I will pay an hefty price premium to have it. But I simply don't like the X10SAE legacy IO, and the uncertainity of what Chipset Stepping you will get. X10SAT guarantees me a C2 Chipset, which most others options do not. Besides, there isn't a lot of variety of C226 based Motherboards, and from all those I looked, the X10SAT is the one that fits me the more. Q87 variety is even worse than C226, and Q87 is one step behind C226 feature wise.
X10SAT is far from perfect, there do are many things that I don't like from it. Besides Thunderbolt (Through that is by design - I suppose any other Motherboard with Thunderbolt will have similar bandwidth issues), I don't like the PLX chip because usually is a bit harder to do passthrough of devices behind it. I don't like neither to have extra Controllers like the ASMedia Sata Controller that can their own quircks when compared to the Chipset IO, and also the fact that it has only 6 slots when it could have 7 (Which X10SAE has).
If you picked the X10SAT, removed Thunderbolt, the ASMedia SATA Controller, the 4 Port USB3 Controller, and the PLX chip, you would have 6 PCIe lanes free (From the 8 max, 2 are used for the NICs).
Intel Chipsets flexible IO can allow you to repurpose 2 PCIe lanes to 2 USB3 Ports (As X10SAT has 4 from the Chipset), so you could have 6 USB3 using only the Chipset, which I think should be enough. With the free 4 PCIe lanes, you can feed 4 PCIe 1x Slots, for a total of 7 slots. I would love such arrangement, its minimalistic in components (As you rely 100% on Chipset, eliminating a lot of possible quirks or compatibility issues), simplifies designs, yet should have enough IO.
X10SAT doesn't have IPMI or the dedicated NIC for it. It seems to be reserved to Server Motherboards, X10SAT is a Workstation one.