please start new topics for new conversations. You are entitled!
As far as I understand (this is an IronPython topic, not a Rhino topic, really, per se), sys.path is not used for clr.AddReference, because that is for a .Net assembly, not for a Python package/module.
However, when searching for a reference fails, Rhino is still invoking its own assembly resolver. That one automatically looks into all folders where a plug-in is installed, including the Libraries folder. @will might know more, as I know he has been making adjustments to that lately.
clr namespace there are other overloads, like
clr.AddReferenceToFileAndPath(), etc. You might need to find the right system that works for your particular installation goal.
Possibly this will tell you which library is being called in a particular moment:
Would you check and report?
Are you planning on shipping the GHPY aside the other .dll? Or the GHPY in its own folder, and the other .dll in another?