Something being a singular being in the multiverse does not prove it is the most powerful thing in the multiverse, and it definitely doesn't prove it scales to the Chrono Navigator.
The discussion about power absorbtion was not meant to imply anything about AP. It was being used as an example of why claiming someone "is in no way or respect or manner above the Celestialsapiens" is not a relevant argument. Something does not have to be a reality bending super alien in order for it to be argued that they could feasibly become a threat of the same level or greater by exploiting a trait unique to them.
The Chrono Navigator is also clearly never described with words lesser than those used with Celestialsapiens- at least not in the quotes I've been shown thus far. In fact, I'd argue it looks quite the opposite. Celestialsapiens are repeatedly called "the greatest power in the universe" and consistently described as capable of changing, affecting, and seriously warping "the entire universe" while the Chrono Navigator is described as a threat to "all time and causality itself" or capable of giving "dominon over all space and time" or "every timeline and every alternate reality." Those are much heavier words being used to describe the Chrono Navigator. It's true that Professor Paradox never calls the Chrono Navigator "omnipotent," but there are two different problems with that.
First of all, it would be unusual to call a tool "omnipotent" just for being capable of ending all of time and space in the first place. If you had a button at your disposal, for example, that when pressed, would destroy the entire multiverse, all of time, and any conceivable reality, it would be considered weird to call that button "omnipotent." The word usually implies more versatility than that, like the ability to delete gravity and suddenly give yourself wings and turn the sky purple while having a conversation with George Washington on Neptune as classical music springs to life out of nowhere. Can the Chrono Navigator do anything like that? I know Celestialsapiens can, but it was my understanding that the Chrono Navigator was solely destructive in this scenario, along with the ability to teleport and travel through time. It can't like... turn me into a bag of cheetos with laser eyes while bringing Bugs Bunny to life to play Half-Life 3 with, can it?
Secondly, the word "omnipotent" not being used on something does not necessarily imply that it's not omnipotent. If, for example, you told me now that the Chrono Navigator actually ca do all of the crazy things I listed above, then that alone would still not be solid evidence that Alien X is more powerful than it is, because as far as I can tell, the Chrono Navigator's full capabilities were only discussed once. It would be folly to argue that Alien X is more powerful than the Chrono Navigator just because over the course of four different episodes Celestialsapiens were called "omnipotent" twice while the only discussion about the Chrono Navigator didn't use the word "omnipotent." That's rather silly.
I do apologize for misunderstanding about the "specific circumstances" however. I think something someone said earlier might have gotten me a little turned around. I should really watch the episode myself before commenting here again.
I don't really have any particular issue with Alien X or Celestialsapiens being upgraded. I'm about as neutral on the subject as possible. I just came here because I remembered liking this show when I was younger, but I still don't think these are very solid arguments. I'd lean more toward your side if it weren't for the dates associated with each quote, but it is very concerning that the argument boils down to "Celestialsapiens should be more powerful than the Chrono Navigator because Professor Paradox called them 'the greatest power in the universe' over two years before the Chrono Navigator was written as a weapon capable of destabilizing the multiverse." Like... it's not inconceivable that the writers had things planned out that far ahead and the show was making a definitve comparison between the two. It's not impossible that Professor Paradox failing to call his Chrono Navigator "omnipotent" during his one explanation about it was meant to be a clue that it isn't as powerful as a Celestialsapien. But it seems really shaky. It would be super useful if you had some quotes from Professor Paradox restating that they are the greatest power in the universe after the plotline that established the power of the Chrono Navigator, but without that or some more definitive comparison between the two, I can't personally find myself agreeing with anything beyond "At Least Low 2-C, Possibly 2-B." And I really don't think I'm being unreasonable. I'm sorry if I made people upset, but unless I'm misunderstanding something, it really, really looks like you're trying to scale something to something else by use of some pretty shaky statements, written more than two years apart, that don't correlate to one another.