You seem to be misunderstanding how PCIe lanes work a bit. The CPU provides lanes and the board has PCIe connections that utilise those lanes, but it doesn't provide lanes for each connector on its own. The chipset on the motherboard will provide some lanes as well (the amount depends on the chipset).
Typically, CPU lanes are reserved for high bandwidth devices. This basically works out to be reserved pretty much always for graphics cards. Things like storage, add in cards and such will run off the chipset's lanes.
Your Thunderbolt add in card should take up some lanes from the chipset, not the CPU, meaning the graphics card's lanes will be unaffected. Even if it did take some CPU lanes and dropped the GPU down to PCIe 3.0 x8, it wouldn't impact performance as the GPU can't fully utilise PCIe 3.0 x8 anyway.