Yep... Though I don't think I'd have the bottle to discuss butchering one of their materpieces.
....Well, I expect they would confirm my thinking (in ignorance of the technical details) that it would interfere with the flow and therefore they wouldn't be able to support their product guarantee. I'm sure that Milltek wouldn't be unfriendly to you though if you contacted them.
I'm sure they wouldn't advise it but the bottom line is that it is yours to do what you want with. However, I think it might be easier for you to buy a second-hand Milltek twin pipe backbox section.