You can even place your siteconfig.pm in a custom directory (or just link it thereto), e.g. X:\myconfig\perl and set PERL5OPT to -IX:\myconfig\perl -Msiteconfig, so you don't have to mess with installation paths at all.

On my system (Linux):

# file /tmp/perl/siteconfig.pm
print "loaded " . __FILE__ . " from $INC[0]\n";
shift @INC; # done with files in /tmp/perl
1;
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qwurx [shmem] ~> env PERL5OPT='-I/tmp/perl -Msiteconfig' perl -e 1
loaded /tmp/perl/siteconfig.pm from /tmp/perl
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The shift @INC restores the original @INC perl lib search path array. Comment it out if that config directory contains more of your custom modules which should be found first. This is all in perlrun, which is worth reading thoroughly.