I use Debian, and I use an option you didn't list.

I use the system Perl (threaded 5.8.8), and I install all my packages in a fresh directory using cpan (although using cpan is not required).

• Set makepl_arg to PREFIX=~ LIB=~/lib/perl5 (Any version of MakeMaker)
• Set makepl_arg to INSTALL_BASE=~ (Alternative for MakeMaker 6.31+)
• Set mbuildpl_arg to --install_base /home/ikegami (Might accept ~)
• Add export PERL5LIB=~/lib/perl5 to ~/.bash_profile
• Run mkdir -p ~/.kde/env && ln -s ~/.bash_profile ~/.kde/env/profile.sh (For KDE console login)

(The following setup uses ~, but you can use any directory. I don't know the equivalent of the last for gnome.)

I haven't had any issues yet.