MTH has already done a couple of Old German modern reefersand at least one American Beer modern reefer, so they might be your best bet, if you could somehow show them there is sufficient interest in these other brands. Their Premier 36' woodsided reefers are just as good as Atlas' IMHO. I know that I would be interested in more good-looking Premier woodsided reefers (their recent offerings have been rather bland).
A LHS might also be interested in sponsering a custom run, again, if they thought there was sufficient interest to recover their investment quickly (remember that in most cases, these cars, if done by anyone other than a manufacturer, have to meet minimum production run criteria and have to be paid for in advance - before production is started).
A big problem with this type of thing is getting permission or licensing to use the brand and logos.
As for an individual to attempt something like this, well, after following, from the beginning, Paul's experience getting the Natty Boh cars done, I don't think you will find someone with the guts to try it as a solo project, and the perserverance necessary to see it through to completion.
Andy