The FPS penalty is not a result of the bandwidth limitations, its the overhead and latency of the Thunderbolt controller. If you ran a GPU from an x4 slot normally there would generally be no performance penalty at all(at least with with mid tier cards at 1080p on most games), but once you have to go via a TB controller you generally get a fairly persistent hit, so it's the controller really where the issue lies, but Intel have started to let people make their own now. Though having more bandwidth would help once you start to move up to higher resolutions as usual.
Personally run my eGPU off a PCIe2.0 x1 Expresscard line though and generally get less of a performance hit than I would using TB3(PCIe3 x4 so 8 times more bandwidth and less performance), but that's an RX460 at 1080p tops.