In regards to that, it's a part of the translator's own references to that stuff. Something I have seen there was some kind of way to know "it's used in the sense of superiority", when that isn't something that is really possible to say just by grammar, it's something with context. In the same way that there's no single word in English to be used in regard to "transcendence in the subject of superiority", there's also no way of saying that in Japanese.
Take the Koeru subject again, technically there are two kanjis that correspond to that, one that means "moving across, to the other side" and one that means "beyond", and yet there's a lot of moments where the Kanji with the sense of "Beyond" is used as "travel across", is a nuance in works of fiction that aren't really represented just if you use the dictionary.
Take "Kukan" (Space) as an example. It's a word to describe physical space as in the three-dimensional world we live in, yet there are a lot of moments when it's used as a generic word for "a different dimension, universe", something that Pokémon does a lot and I explained on my blog due to Palkia ruling over "Space", that includes "parallel spaces" that are the way they call parallel universes.
Asking those translations without knowing the context is always a double-edge sword.
In regards to the use of transcendence, I would say that the way that the creation myth is explained it always made sense for me for the Mind to be transcendent over time and space itself, something that is mentioned in more than one place (For example the statue in Pokémon Mystery Dungeon Explorers of Sky) and it makes sense to talk about the omnipotent creator of the universe that at the same time is everything in space-time and also is beyond that. But if we are talking about very direct mentions about being "infenitely stronger" similar stuff, I don't think it's possible to get that.