Quick and dirty option: add a symlink to your modules into an existing perl include path
The OP mentions using apt-get install, which strongly implies he's using a Debian or Debian-derived system. A default Debian install will have /usr/local/lib/site_perl in @INC for precisely this purpose. But this does, obviously, make any modules linked there available to all users on the machine rather than user-specific, which may or may not be acceptable to the OP.

Really, though, the only real problem I see in the OP is the bit about the user's $PERL5LIB carrying over to root when using su. My solution to that is, quite simply, to use sudo instead, as it does not carry over the original user's environment: 

me@host:~$ export FOO=bar
me@host:~$ echo $FOO
bar
me@host:~$ sudo -i
[sudo] password for me: 
root@host:~# echo $FOO

root@host:~# exit
logout
me@host:~$ sudo bash
root@host:/home/me# echo $FOO

root@host:/home/me#

[download]
If you prefer su over sudo, you should be able to get the same effect by using su - or su --login to open a login shell with a fresh environment instead of preserving the previous shell's environment. From the Debian 10 version of man su: 
       For backward compatibility, su defaults to not change the  current  di‐
       rectory  and to only set the environment variables HOME and SHELL (plus
       USER and LOGNAME if the target user is not root).  It is recommended to
       always use the --login option (instead of its shortcut -) to avoid side
       effects caused by mixing environments.
and, from the Debian 8/9 versions of the man page: 
           Note that the default behavior for the environment is the
           following:

               The $HOME, $SHELL, $USER, $LOGNAME, $PATH, and $IFS environment
               variables are reset.

               If --login is not used, the environment is copied, except for
               the variables above.

               If --login is used, the $TERM, $COLORTERM, $DISPLAY, and
               $XAUTHORITY environment variables are copied if they were set.

               Other environments might be set by PAM modules.
So just add --login to your su command and $PERL5LIB won't be carried over to your root shell.

In reply to Re^2: Best practices for local libraries by dsheroh
in thread Best practices for local libraries by Barrabas

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