No, you can't tell the newer version of Unison to pretend to be an old version. This is a notorious feature of Unison; the format of the archive file (that keeps track of everything being synced to improve efficiency) gets ~~changed~~ improved in each new version. So Unison versions across machines have to match precisely.
Since 2.40 is an older version I'm not sure if it would be in the Ubuntu repos. You could compile and install it from source, or try one of these pre-compiled binaries.