If I understand your question correct that is; why not install the application for a specific user?

Users in a corporate environment usually are standard users (non admin-user) so for any user being able to use the application we install it as "per-machine" or as you called it "System Context Windows".

Most of the deployment tools like SCCM, BMC CM, Altiris, install/deply the application to the users in company though System context. This is the elevated user with privileges to install the application with admin rights.

I presume that you are testing the application by installing them in System context. This is to make sure that the application will work fine when installed through a deployment tool. You can simulate the installation from a deployment tool in your test machine if you install the application in System Context. You will get to know if there are any issues beforehand.

Hope it helps clarifying your issue.

Cheers,

Piyush

Check the license agreement for pretty much any application and you'll find that in general it will be licensed for a machine, not a user. If you install per-user, you may find your company in the position which an ex-client found itself in: 70 licenses for Microsoft Project and 678 installations. Oops!