I cheat

I put the FULL URL I want to use in the configuration file, then change the code in Context.pm to take that as a literal instead of appending it to the cgi path.
The sub below replaces the sub of the same name... note, it works for me and is only temporary till MT moves to a more flexible URL definition configuration.
CODE
sub _hdlr_entry_tb_link {
my $e = $_[0]->stash('entry')
or return $_[0]->_no_entry_error('MTEntryTrackbackLink');
require MT::Trackback;
my $tb = MT::Trackback->load({ entry_id => $e->id })
or return '';
my $cfg = MT::ConfigMgr->instance;
# my $path = $cfg->CGIPath;
# $path .= '/' unless $path =~ m!/$!;
# $path . $cfg->TrackbackScript . '/' . $tb->id;
my $path = $cfg->TrackbackScript . '/' . $tb->id;
}