xf86-video-nouveau-1.0.12 needs a patch to support more than one monitor in a reverse prime setup with the current xorg-server. See https://bugs.freedesktop.org/show_bug.cgi?id=93670 for details. The fix is already in upstream git, but there is no release with the fix yet. Upsteam commit: https://cgit.freedesktop.org/nouveau/xf86-video-nouveau/commit/?id=b824d36c28124955eda4aced5e637aa75eea4d6c Please add the patch to the ebuild.
Ilia says that this should be fixed in 1.0.13, which is now in the tree. Please test and reopen the bug if it is not fixed for you.