Does SCCM support dependency provider keys? If so, Python 3.6.0 and 3.5.3 and later will set one of these (see issue28846), which should make it easier to detect the whole bundle. Previous versions of 3.5 used a random GUID here.

I managed to reproduce the issue on a test machine by running a per-user install as admin, then the per-machine install. I tried a few ideas to treat the per-user and per-machine installs more distinctly, but nothing seems to work well. Most likely, I'll just have to add a more serious block when there's an existing install and prevent the second bad installation, though I haven't yet figured out how to do that.