Yes, it seems to work. Last time I tried it I ran into some problem, the mask layer didn't work even though the paste layer did work.
To the original poster: if you still need to edit those footprint text files manually you can try to change the pad number of the paste layer pad and mask layer pad to "" (empty quotes). That's how they appear in my footprint file. It's certainly easier than moving the mask and paste layers to one pad. However, you will loose the possibility to use global mask and paste size settings which may not be what you want.
If you can and want to use the footprint editor it's easy to delete the extra pads and add the two layers to the copper pads.