Well the way I do it is to call the chmod contained in the cygwin package recursively on all files later passed to mkquashfs (so I call chmod.exe -R 755 [folder to compress]).Are you talking about running chmod via cygwin on all the extracted files prior to opening? It would be nice if calcs could be used to set all these permissions.
I dunno whether that is the best way to do it, but it surely works.