Probably not. The way TSO works in network interface cards is that the software hands over a big packet and then the NIC slices it into MTU-sized chunks. In that case, lowering the MTU makes no difference at all to the sending TCP stack, which is in charge of setting the transmit rate.
But I suspect what’s happening with Thunderbolt networking is that the segmentation step is simply skipped. In that case the MTU value is completely meaningless.