This isn't borne out in the background though, and that makes sense because it is impractical to force every feudal or feral or frontier world to learn Low Gothic. The Ecclesiarchy (despite their best efforts) isn't universal, and many, many other sanctioned sects of the Emperor's worship exist. As already pointed out, when a planet is colonised, rather than outright destroy the existing religion, they nudge it to become a version of the Emperor-worship. Things like 'Well, this god you are worshipping, you see, he is actually the same as the Emperor, so you should just start calling him that...'. Very much like how real world religions have done it- Christianity would have been a much harder sell to pagan Europe if they didn't do things like take the pagan Midwinter festival and turn it into Christmas (and be damned when Jesus was actually born in the year). Only the larger, important planets have a proper Ecclesiarchy presence.
As it stands, background stuff tells us that Low Gothic isn't universal- Fenris speaks fenrisian, Tallarn speaks it's own languages, even Armageddon clearly has a heavy distinction between dialects from the Primus and Secondus continents, as shown by Helreach.