The gateway options are part of the Windows Registry. Some programs are impolite about cleaning that up when they're uninstalled. You mentioned having a couple D2 folders in the future, in which case I'd recommend using D2SE for the moddable D2 folder. I'm pretty sure D2SE doesn't require mods to edit the registry for their gateways since that information is stored in the .ini file for each mod. When you get your next version of HU compatible with D2SE, don't run d2modsetup.bat since that isn't necessary for D2SE and I think that results in the gateway changes in the registry.
This tech support thread seems good enough for solving the issue:
http://forum.arimyth.com/viewtopic.php?f=9&t=21168