Shouldn't putting them all on one line work? Like

o conf makepl_arg LIB=/path/to/my/distros/perllib PREFIX=--perl_only

Usually, everything but the last configuration gets dropped. Usually.

Update: Or edit ~/.cpan/CPAN/MyConfig.pm directly and set the things you need from there. I'm changing the configuration while in the CPAN shell to download CPAN modules to a specific location, so I can then add the modules to a distro. Basically.