I ran into this exact problem today. In my case, my Z87OSX system had two GPT formatted HDDs. Initially, one drive (disk0) had a macOS Sierra install and the other drive (disk1) was HFS+ formatted for data. I followed the multi-boot instructions and resized the HFS+ partition on disk0 to provide space for the Win 10 install.
However, when I ran the Win 10 install, it refused to install, issuing the same message reported earlier in this thread. I had to unplug disk1 and then run the Win 10 install. This all suggests that the installer is not confused by an existing Windows install, rather it is confused by more than one GPT formatted disk being present. One possibility is that the Win 10 installer assumes it is installing in a single disk environment (which probably is the typical configuration).
Whatever the case, it seems easier/safer to disconnect all but the boot drive when building a multi-boot drive like this.