The installer is designed to work that way. Multiple installs of the same version of the runtime engine should only increment the reference count on the files. When you install your built application you will not see an entry for the runtime engine in the Add/Remove Programs (ARP) list.
If you are familiar with MSI terminology, this behaviour is because the LV RTE that is included in your installer is just the merge module not the MSI. When you install the LV development environment, the RTE is installed from a separate MSI. Because your built app installer will use the merge module, the only way to uninstall the RTE will be by uninstalling your app.
Naren