The resonators probably do make a difference. If you were to remove them you'd probably notice some time of drone or whistle that wasn't there before. I would leave them on because they do not inhibit flow.

As for the discoloration it's probably because the resonator has a wider diameter than the rest of the piping. Which means that there is more metal to distribute the heat and results in less discoloration.

They appear to be quality built headers and you can't really screw up long tube design.