I can confirm two things:
1. Code 43 still occurs on Windows 8.1 (at least on a Thunderbolt 2 eGPU setup). So Windows 8.1 is not a solution.
2. The registry entries that Nando hinted at aren't referenced at all during the install.
I recorderd all registry reads/writes during installing the drivers and there is no reference to Hot plugging, Removal, Restarting, Resetting, etc. So this seems hard coded into the drivers, and not something that can be turned off via a registry entry.
Unfortunately, no solution thus far for Thunderbolt eGPU users, and those without BIOS access to PCI-e hot plugging settings.