I am not sure that this is really an issue, rather than a process suggestion. I totally understand the Fireworks style workflow for slicing for things like logos or graphics that you want to export with an alpha channel for placement over graphics / colours in CSS.
In the export Persona, there is a tab next to "Slices" called "layers" - I switch to that, and go through and turn off the layers or even specific graphic items that I want to be visible or not in the export. This works well enough, but...
It would certainly be more useful to be able to define what ares of a slice you want to be the "mask" - i can't really sort out what the point is at all of the current "Matte" colour is used for on the slice Export Options tab - it doesn't really seem to do anything regardless of what I sample there. For example I can have a very simple slice area, white logo, single colour background. I set the Matte value to white... exports the logo just like it was a jpeg... set it to the background value... exact same thing. I don't know what the matte value is supposed to do in the export persona, but it doesn't seem to do anything.
However- I think the bigger thing here is more the workflow when choosing what elements of your layout / graphic to include in your slice.
This is not a real "issue" since keeping things organized on layers is good for all kinds of reasons, and turning them off at time of export is not a big deal, and I find the process of switching between the layer tab and the slices tab to be fairly easy, albeit a little tedious.
Ideally... in the actual slices detail - I could define right in that slice what layers to include in the export - so each slice area is customizable.
I don't think this is really a big deal - I can get the proper transparency with the current build, but it's a little clunky. And I would certainly be open to some explanation as to the intended use / function of the Matte value when setting up a PNG slice.