Hmmm. I hadn't seen that how to.
It might be possible to make it work, however you would have to make links to every directory where the new application has files...all libraries, executables, etc. The links to the new /etc, usr/bin /usr/lib et al directories containing the new application files would have to append to, not replace, the existing directories or else your existing applications would not work.
I think this is essentially how klik applications work but I could be wrong on this. Check the information on klik, there may be some hints as to how to make your own klik-type installations.