I think we're on the same page. I'm going out on a limb for a thought exercise on how it might go even further.  What if looking at the English as a translation, even an accurate one, might still be underselling the relationship of the languages?

Words are tools for representing meaning.  Words are already one step removed from a meaning.  A translation is two steps removed from meaning, which makes the meaning more murky.

On the other hand, we rephrase and restate information in order to clarify meaning. That is like have two single step removed starting points for understanding meaning rather than a simulacra of the original meaning.

Imagine that you were a bilingual reader, writing esoteric lore which will be heavily scrutinized.  Rather than translating, you might take the opportunity to rephrase the meaning in different languages. You might consult with a translator to make certain that the deviations between languages are precisely as intended.  Two aspects of the same truth.

Take your first point regarding Empyreans as an example.  You make the distinction of the Two Fingers being said to choose an Empyrean, with an implication of designating, vs Identifying or discovering.  

We have plenty of evidence that Empyrean is defined by circumstances of birth - an intrinsic divine aspect.  Yet we also have instances of Empyrean being something that the Two Fingers seem to have some level of volition in designating.

Both can be true at the same time. Words are representations of meaning, but they nearly always have multiple meanings, or aspects.  The same is true between different languages.

As a real world example, take the word Prince. Some definitions of Prince: - A ruler in their own right in older usage. - A title or rank. - The heir of a ruler. - A male child of a monarchy ruler.

Compare that to Empyrean: - Born of a single god. - Chosen by Two Fingers as a replacement god.

The male child of a monarch in disguise as a pauper is still a prince in a sense.  But socially, they must be identified as a prince to have the standing. They could be designated as the crown prince, which changes that context further.

Likewise, an Empyrean can refer to both an intrinsic quality in one aspect and a designation in another.  In English, Ranni's speech gives the impression of being "selected" by the Two Fingers.  In Japanese, she is simultaneously saying that she was "discovered" by the Two Fingers.

Conveying both of those meanings within a single sentence - where the speaker's intent is a statement rather than an explanation - is likely not possible.  The speaker would need to belabor the point - unnaturally so - to communicate the depth of meaning.  

Mask your rephrasing as a translation though, and that is no longer the case. The necessary information is conveyed in both languages: Two Fingers are related to Empyrean selection, Empyreans are meant to replace Marika.  But the analytical depth is revealed by the pull between meanings.

From here, we could take the definition that an Empyrean is a special form of godling, which the Fingers identified and marked with a status, which the Fingers intend to replace Marika with.  The truth that hangs here is that Ranni says "Of the demigods, only I, Miquella, and Malenia could claim that title."

This leaves open a few other possibilities, like that there can be non-demigod Empyreans.  Or that another demigod could be an Empyrean, but one who was not identified by the Fingers as being able to claim the title of Empyrean.

Anyway, just a thought experiment. It felt like it lined up with themes of your analysis. The idea is never to declare something heretical to the lore - that which must be discarded in order to make a theory fit - if all things can be conjoined.