The "Publish in" filters do apply to both Main Dictionary and to Reversals.
Normally the "Publications" would be for things like, "Webonary", "student dictionary", "academic dictionary". The assumption is that any of these publications might want to include both the main dictionary and a reversal index, and the filter just controls which entries get included, along with their links from main to reversal.
One option is to set up two different publications, and then do two exports. Both exports would export both the main dictionary and the reversal, but you would choose the main dictionary from one export and the reversal from the other export.
This assumes that you are exporting on your computer and then will do something to publish those output files, either as PDF, or through Word/OpenOffice, or some other means.
If this is for uploading to Webonary, you can only set one Publication for the upload, and it will apply to both. There might be a way to manually adjust something, or we may be able to come up with other ideas.
-Beth