Usually most people get concerned with twist and bullet weight, not number of grooves, it'a nice to see an unusual question. But if your going with a custom barrel, it's nice to have both options, and I don't know till recently that number of grooves could be specified.
While I don't have the answer, I know a guy that's built up a rifle (sorry I don't remember the caliber) who indicated that because he was pushing the slug pretty darn fast, he had gone to a 3 groove barrel because it allowed him extra speed without the friction/heat build up of a 5 groove. He was claiming very good accuracy and felt that he'd get better barrel life. The discussion was more technical than that, but it's been a while.
I'd probably ask this question to a barrel maker for the best answer, but it will be interesting to follow this thread for an answer. There is another thread within the last year about grooves, you may want to read that information, though it didn't answer the question completely for me.