Michael, I know exactly what you mean. I wondered the same thing for a long time, whether the orange mask would make separations difficult. But along with what Ron is saying, it's not a problem.. something I was quite surprised by!
I actually have in front of me a copy of Wall & Jordan's 'Photographic Facts & Formulas' from the library, and it explains this very well.
Basically, the orange mask is a product of two separate masks. In the two layers that require masking (cyan & magenta), the couplers are made to be colored themselves. Upon processing, the colored-couplers are destroyed where the image density is, and left to remain where there is none. Thus, the coloring matter is inversely related to the dye image.
Cyan has unwanted blue & green absorption, so the coupler in this layer is reddish and acts to mask these unwanted absorptions. The magenta layer has unwanted blue density, and the mask here is made to be yellow.
Interestingly, as is the case in all printing schemes as far as I know, yellow is good enough to not require masking. Damn that yellow...
Now if that wasn't enough, the dye-transfer printing matrices must also be masked to account for unwanted absorptions in these dyes. So first you have to get good clean information from your separations, and then you have to "unmuddy" the waters again during printing.