It was an in-joke for fans who had seen "Broken Bow". Travis says to Malcolm, when beaming up cargo that Archer "Wouldn't even put his dog though this thing".
He shouldn't have changed his mind!
But actually I got the vibe from the film that Scotty did it without Archer's permission.
I'd assume the dog in STXI is Porthos XXIV (or whatever), but you could always say that alien liver transplant from "A Night in Sickbay" gave him alien lizard super life expectancy
(Also "not very canon" is wrong. If it's on TV or film Trek it's 100% canon whether it makes sense or not!)