It shouldnt matter mathematically the route is a bit different but the end effect is the same. However your description tells me your not talking of what you think your talking.
However please note when you make a matte for something thats not the images original matte. IT always works straight because thats the definition of mattes in adobes thinking (adobe turnes everything straight for computation). So your no longer in file reading realm.
QUOTE
Should I render my Mattes as straight unmatted?
well the way you describe it wouldn't matter one way or other, not n the realm of the problem. When you use then as mattes later on the color channels would cease to have any meaning (you should in all actuality skip the color entirely).
could you describe in quite exact words what your work flow is it would make more sense.
The you end up with masking and matting problems it mostly about the mathamatics behind it you dont understand
PS adobes greatest strength is also at the same time its greatest weakness, see the fact that user needn't know internals is a good thing in general until you suddenly start to need things at that level at which point the foundation of the strength drops away. Its a either or thing, if you have both you end up with a situation that confuses the former layer too much for any significant benefit. Because then suddenly you start to nee dto know the things because they now and then pop up.