Yeah, I too was perfectly fine with it (Omega as og Omega was "dead"/outside of influence after all, and this Omega was ever-existing outside of time with a lot of influence & in line with sessional arc about god magic) ...

... but generally speaking - if they even bothered to offer an explanation (which in this case they did, it was central to the plot), I feel like I should be happy/glad with the matter as in so many other cases (Doctor Who too, but I mean mostly other such universes) change previously known things significantly (just to "look cool" as the sole goal & noting else) & don't offer anything in return, not even a background hint for an explanation.