Python\'s access to environment variables does not accurately reflect the operating system\'s view of the processes environment.
os.getenv and os.environ do not func
I don't believe many programs EVER expect to have their environment externally modified, so loading a copy of the passed environment at startup is equivalent. You have simply stumbled on an implementation choice.
If you are seeing all the set-at-startup values and putenv/setenv from within your program works, I don't think there's anything to be concerned about. There are far cleaner ways to pass updated information to running executables.