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Nick is the authority on -m so perhaps he can confirm this but I believe the execution of -m is carried out by the runpy standard library module and the runpy module essentially goes through the process of finding a module from scratch by searching through the modules in sys.path, thus bypassing the altered sys.path which the setuptools/Distribute site module "bootstrapped" and removed itself from. So runpy will always find the setuptools/Distribute site module first since it is first on sys.path (until it executes and removes itself from sys.path). It seems you've found one case where the sys.path manipulations of setuptools/Distributes make a difference: when trying to run site itself. You can see which site module is found by runpy by trying:
 import runpy
 runpy.run_module("site")