Curiously, I'm wrestling with this very issue right now. This approach just isn't any good unless you can be sure that the Perl in the shebang line has all the same mods installed as the custom installs you're trying to execute.
We have a Perl script that we require in a BEGIN block for each script we run, and we'd have to both make sure that the #!/usr/bin/perl has all of the mods that we're using in the script otherwise it won't compile, and we'd also have to evaluate the require once for the #!/usr/bin/perl and then again for the script running under the correct Perl.