I am not sure how to solve your installation creation problem, this is more advice that maybe you should not be trying to solve the problem this way.
Just guess here, but having two separate applications probably means you have two separate main VIs (that are very similar as you mentioned).
This may work fine in the beginning, i.e. your application is stable and then you hide/show some controls and save a copy as a new VI, but eventually you will reach a point (as more and more *features* get added in) where it will just become extremely troublesome to have two separate VIs, and each time to build two binaries.
Instead, why don't you have some form of user login, and have the controls dynamically disabled/enabled depending on whether a user/superuser is logging in. That way you only need to design/maintain one main VI and it makes further improvement down the line much easier.
Neil