Yes, as far as I understand each of them should be separated by 3mm. Take a look at the document section 7. https://communities.intel.com/servlet/JiveServlet/previewBody/23158-102-3-27299/edison-module_HG_331189-001.pdf
Sorry, I should have phrased that better. The question is whether every board in the stack has to have a blank area for the keepout zone, or whether that only applies to the board closest to the Edison. The keepout zone occupies a significant amount of board real-estate (and board edges, where I'd like to mount connectors) so if I can skip the keepout zone on boards that are further away from the Edison then that would be great.