Try adjusting the master page using pages tool.
Bob is correct. In InDesign CS6 and CC, the Page tool is the way to do it. Document Setup can't really handle it because you can now have multiple page sizes and orientations in an InDesign file.
Select the Master Page(s) in the Pages panel, then use the Page tool to adjust the size. The 9-point proxy determines how the re-sizing is accomplished (from which size or corner the re-sizing is applied). Be sure to ask if you have more questions.
I understand the multiple page sizes, but those fall out of the realm of the "document size" and don't change if they've already been adjusted manually outside the origional document size.
Doing a double take thinking maybe my memory was off, I tested it out in CS6. It worked pretty much how I remembered by centering the document instead of aligning it the upper left, just didn't align it wherever I had it set othersize. I guess I will stop having to be lazy if I have one document size and adjust using the tool on the master page. Just kind of makes sense that an overall standard document size change would have the page centered, versus aligning to the upper left.
Also part of the Control panel controls for the Page panel is Liquid Layout rules. If you choose Re-center, it will automatically center the content on the new page size.