Config options (and Makefile.PL/Build.PL arguments) control everything, so the best way is to fake MyConfig, example mycpan

#!/usr/bin/perl --
BEGIN {
package CPAN::MyConfig;
$INC{'CPAN/MyConfig.pm'} = __FILE__;
...

};
my $cpan = 'path/to/cpan';
do $cpan;
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I got the idea from Re: CPANPLUS custom configurations. See also mkmyconfig, Install a CPAN module at x location, Personal library with CPAN, Installation of modules in home directory, install_base.