I think you're doing something wrong if you need to switch to root just to locally install a module into a directory you (as a user) should have write permissions to.
Personally, I wouldn't run any "special" applications using the system Perl, because using the system Perl couples your application and the system together into one upgrade cycle. I use my own private Perls installed under /opt/perl/ and compile all modules needed for my applications for them.
My golden rule for messing with the system Perl is: Everything that goes into the system Perl also needs to come from your vendor. For Linux, this means that you should only install modules for the system Perl using the distribution package manager. Everything else will break not only your application but also many other system utilities in the long run, because vendors and distributions like to meddle by applying small changes to stuff, which tend to get overwritten when installing other stuff from CPAN.
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