Afaik a regular system does not have an /usr/bin/unison binary (due to slotted installs). If you connect to a remote station (both running Gentoo) it tries to call unison but fails due the missing file. My quickfix was to symlink unison-2.32 to unison, but that's not handy for multiuser. Is it possible to try for "unison-2.40" and then "unison" on the remote side (given local unison is unison-2.40)? I did not find any hint for config values in ~/.unison/*.prf
you will need to run, for example, eselect unison set 1 seems that we can run this from within a ebuild.
actually there is already a message to user to set this up pkg_postinst() { elog "Unison now uses SLOTs, so you can specify servercmd=/usr/bin/unison-${SLOT}" elog "in your profile files to access exactly this version over ssh." elog "Or you can use 'eselect unison' to set the version." }