The commonalities in widely varied tech in even adjacent systems, the rabid anti-psionic attitudes, the marines as battledress, the locally raised army troops being carted off to fight elsewhere, the strong nobility, the rampant inhabitation of inhospitable worlds, the rough upper tech level (TTL 16 for the 40K universe, due to matter transmission); cheap and easy gravitics and fusion, local autonomy of nobles, massive bureaucracies, age of sail ship thinking, Merchants as the primary spacefarers...
Calling it an ATU is a humorous but mild exaggeration. The parallels dwarf the much more visible differences.
Differences including the inquisition and religion-based modality, and 38 thousand years from now rather than 3800, and the neo-latinism and neoludditism. Then there are the fantasy port-over elements: Elves, Dwarves, ratlings, Orcs... Demons...
Its origins clearly lie closely intertwined with traveller. It rapidly grew away from Traveller, but it's close kin setting-wise. (As much as f not more than the Iron Empires setting by C. Moeller, who admits Traveller being the inspiration for IE.)
Apply Occam's razor: it looks and feels like a religious flavor of Traveller. The authors had been official licensees of Traveller, and produced OTU works, too. It's different enough to not be plagiarism, but close enough that the roots of the authors show clearly.