Installing a shortcut only for the current user does not seem like a good idea: what if I install your software under an account that I use only for administrative tasks, such as installing software? Because I try to follow best practices and "Do not run as administrator" !
If you are trying to run one instance of software in the background for the entire system, you should probably write your software as a Windows Service instead of creating startup shortcuts. Wix supports installation of the service .
If you want the user interface component to configure / manage the service to work in the tray, you can then set a shortcut for a separate executable file in the "All Users" folder. Thus, all users can interact with the service, but the service itself is launched only once.
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