Well, perhaps I need to rephrase that. I don't want them to install things where ./configure will normally install things. I want to keep the installs going into a special directory. It is part of a package manager app that keeps track of old installs, etc, so multiple version of say perl can be used. So if the user says:
./configure
make
make install

-> that needs to install in $HOME/apps/metapackage/packagename/packageversion

--so it is not particularly the user say, but the application used by that user, that needs to set all this up for them. The application take conf files the user specifies, and interprets how to do installs for them, by the user specifying install commands in the conf file (./configure, make, make install, etc). When using the app, the user will then lose their power to install anywhere. The application makes them install in a particular area. Otherwise, they need to not use the app.