You can run Unison if you copy the Unison executable to the NAS. Either put it in the default PATH or let the local Unison know where the remote binary is by setting the
servercmd option. You'll need a
unison executable that's compatible with the one on the NAS. If the one from Debian doesn't work (I don't know what libraries are present on Synology appliances), you may need to compile a static binary. Compiling Unison requires OCaml, and depending on which appliance you have you may need to cross-compile an ARM binary (check the knowledge base).
An Ubuntu package should work on Debian too. In fact, an Ubuntu package will work on Debian just as well as Ubuntu; what could make it not work is if the package requires a different set of library versions from what Debian offers (in which case the package would only work with a specific Ubuntu release, and not with other Ubuntu releases of a similar vintage to the Debian release).