Hmm … I am somehow not convinced.
Firstly, I can’t quite see the difference between “they conceive it to be earth” and “they conceive it as earth”. Both clauses say essentially the same.
Also, “they conceive it to be earth” does not render pathaviṁ, earth, as accusative. Accusative is what answers the question “whom or what (do they conceive)?” And the answer to this question is “it” in your sentence; “to be earth” is not an accusative.
The question to which the answer is “to be earth” would be: “How or in which way (do they conceive it; “it” being the accusative object)?” This to my mind amounts pretty much to the same as the “ablative of viewpoint” as it has been explained above, so it would be identical in meaning with the third clause “they conceive it as earth”.
So if you want to refer back to the “percept”—and you are right that the repetition “having perceived earth as earth” means exactly this—you can still do this by adding a reflexive pronoun: “this”.
So the passage would become:
They perceive earth as earth. Having perceived earth as earth, they conceive this earth, they conceive it in earth, they conceive it as earth, they conceive that ‘earth is mine’, they take pleasure in earth.
This at least is my understanding of grammar, mainly the accusative, in general. Perhaps Pali grammar can be applied in different ways, I simply don’t know.