Re: "it is the undisciplined/disorganized installation ..."
Try running yum/apt without sudo privileges, what happens? Linux packages too are installed with high privileges because they may need to setup the system to allow applications to run without high privileges - but the setup procedure may require to create resources in privileged locations and then settings the proper permissions to allow the application to run.
You really have no need to install files in system32 unless you are installing drivers (or maybe a few other system-level modules), and you must not. Writing there has been deprecated long ago and no userland application should ever write there. If one application still does, it's exactly because its developers never understood how to write software for Windows after 1996. A few Microsoft redistributables may write there - but you must use the installer from Microsoft, not attempt the same in you installer. Registering .NET assemblies in the GAC has its own rules.
COM registration must follow precise rules as well, and it's based on GUIDs - if you follow the rules you can easily have different versions of the same component. Office does that routinely, problably because its developers read the instructions...
Biting the hand that feeds IT
