I’ve been spending a fair amount of time thinking about ProtoTraveller, as well as my idea of the “Lost Imperium” setting actually being a Traveler game rather than a Dark Heresy game. Another interesting spin that combines that idea with the canon Traveller universe would be a similar “trip over a Ancient’s trapdoor” during either the Civil War or the Psionic Suppressions.
It doesn’t quite answer the question though – an full-sized WH40K Expeditionary Fleet of the Great Crusade had enough people to found a empire. Whatever it is that meant to escaped from the Traveller universe wouldn’t be nearly so big (ok, I suppose I could posit some other weird Jump Space effect hat simply captures a bunch of ships all at one time or something).
Just something I ponder while I wait for the D&D 5e game to come about!