If Gene said he can play with the frame to get the chainline right, I don't see any reason not to go with the messengers/rd's. That seems to be the only issue I've ever heard of people having with them, and even then lots of people run them problem free. Besides, you can get them on the cheap from benscycle. Also, with the way those chainstays are designed, it seems like there is really no chance of you having your chainring bumping up against them, which might happen with other frames when using the RD/messengers because they use such a small BB to get a good chainline.
Basically, I'd ask Gene and see what he says. If that doesn't work out there are always the IRO/Alien/Andel cranks which seem to be a good buy, and I've never heard of anybody having any problems with them. IMO people spend waaay too much money on cranks in most cases.