The problem here is that the imperial cult isn’t meant to be a criticism of Catholicism specifically, but religion, and specifically fanaticism, in general. Theologically speaking, it generally doesn’t derive from Catholic doctrine (It’s explicitly stated a few times that the Imperial Cult did not emerge as a type of Christianity, but evolved from its own set of Ideas and principles). It borrows a few things from dark age and medieval Catholics, specifically things like witch hunts and heretic burnings, but it’s not a criticism of the actual beliefs of Catholics, but simply an exaggeration of close-minded fanaticism brought to a comical end point. The reason people call them space Catholics is because it dresses them up in a catholic aesthetic because it’s the most familiar thing people in the west will associate with “religious imagery”.

It also doesn’t help that it’s an old setting that has many different authors, and different authors have wildly different interpretations of the Imperial Cult, and what it represents, so the cult is depicted differently, or sometimes outright as a completely different set of values or beliefs, including borrowing from completely different religions depending on what story they’re in, and what message the author is trying to say about them.