I have been reviewing the Install process as we need to start installing / patching Python and I have seen the same issue as mentioned below however the difference for me is I am running the install on a Silent command line.  

I cannot seem to override "AllUsers" Property using the command line as WiX logs the following: "Ignoring attempt to set non-overridable variable: 'AllUsers'."  If this parameter was made overridable I believe this would then allow the Bootstrapper to be listed under all users Uninstall area rather than the current user (or in my case it gets written to HKEY_USERS\.Default\... (which is really unhelpful) as the installer is being run under the system context).