None of this particularly bothers me. At one point, Domino's had an ad that said that there were 75 million possible pizza combinations at Domino's. Someone questioned that number and actually went through the math and concluded that the actual number was really 105 million possible combinations. So, it isn't like someone can't get what he or she wants at Domino's outside of the artisan category. Maybe pizzaboyfan is right and that it is all marketing but there may be practical reasons for limiting the options with the artisan pizzas, such as ingredient inventory control or management or possibly they are testing a second category of pizzas (the artisan pizzas) that they can easily and quickly jettison if it doesn't take hold but can easily expand if it does.
If we look at Brian Spangler's menu at http://apizzascholls.com/Menu/index.html
, his restrictions apply to the Build your own Pie category, specifically, "No more than three (3) ingredients per pie, including no more than two (2) meats per pie". As a highly skilled and talented pizza maker, I have to believe that Brian has a reason for those prohibitions. He also offers several House Pies, so it isn't like diners don't have a lot of options. My view is that if someone is offended by Brian's rules, then they don't have to eat there again. From what I can tell, Brian is still packing them in.
Now, if we look at Anthony Mangieri's UPN menu at http://www.unapizza.com/sf/menu.html
, the entire pizza menu comprises only six pizzas, and one is only offered on Saturdays. The only items on the menu are pizzas and drinks. There is no "make your own pizza" option, and I believe that apart from a possible allergy exception, diners do not have the option of changing what is on the six pizzas on the menu. If that offends diners, again, they don't have to eat there. From what I have read, Anthony is still packing them in also.
Brian and Anthony have found niches that work well for them without offending their own sensitivities. I think for them their craft is more important than trying to maximize their sales and profits.