Rob, have you considered Michael Parks for your commission pieces? He is a super friendly guy, and is certainly skilled and creative. Peck would be able to tell you how collaborative his pipe creation process is; and his work stands for itself. That all being said, I understand that his commissions do take a L O N G time... so that needs to be considered.
Here is a link to Michael's Bulldog Gallery: http://www.parkspipes.com/bulldog/
-- Pat
EDIT - I realize I didn't answer your questions from the OP ... my bad. Here goes.
I have had one commissioned pipe made, so far. I worked with Jeremiah Sandahl from http://sandahlpipe.com/ the pipe he made me is 2013 #54 in his pipe gallery; the two-stemmed cutty. Jeremiah was very collaborative on things like shape, size, materials, and finish, but I was also fairly hands-off once we got through the basics. I wanted him to make me a Sandahl pipe, after only framing up my initial needs and wants. I think when it comes to a more specific need/want it probably makes sense to ring up the makers you think will make a great version of the pipe you want, and then to ask them about their commission process. This will help you get a handle on who you like, and why, and you'll end up getting the result you're looking for.