I think I found the right section of code to change, but my Perl isn't good (it's non-existent). The code snippet is below, from lib/Slic3r/Print/GCode.pm. I don't want to start with $last_extruder_id, but always order it extruder 1, extruder 2, extruder 3, etc.
# tweak extruder ordering to save toolchanges
my @extruders = sort { $a <=> $b } keys %by_extruder;
if (@extruders > 1) {
my $last_extruder_id = $self->_gcodegen->writer->extruder->id;
if (exists $by_extruder{$last_extruder_id}) {
@extruders = (
$last_extruder_id,
grep $_ != $last_extruder_id, @extruders,
);
}
}