Not sure that this applies to what you want to do:

use warnings;
use strict;
use Config;

my $obj = tied %Config::Config;

print $Config::Config{startperl}, "\n";

$obj->{startperl} = "garbage";

print $Config::Config{startperl}, "\n";

__END__
outputs:

#!perl
garbage
[download]

That's a technique used by ExtUtils::FakeConfig. If you want a hard coded Config.pm with altered values it might be safer to use ExtUtils::FakeConfig. It creates a Config_m.pm with the overwritten Config values. If you want to use those overwritten values, you invoke perl with '-MConfig_m'. Otherwise the original Config values are used. ExtUtils::FakeConfig was written with a view to overwriting some specific Config values, but I think it can fairly easily be generalised. Could be worth a look.

Cheers,
Rob