I haven't got my HoME handy... but going by memory, I think your problem, or confusion, comes from identifying Arda with "everything that was created from the Flame Imperishable." At least in his later works (cf. Morgoth's Ring), Tolkien associated the Kingdom of Arda not with all of creation, but with the Solar Syst em. Of course, this sort of throws out the cosmology of the Ambarkanta...
I hesitate to say much more than that without my books handy, but essence of the matter is that Tolkien himself changed his mind about the cosmological nature of Arda (and its place within or complete identification with creation), and different passages in the Silmarillion might hail from different stages of its development. This comes into play with your Eärendil question--not least because the texts on Eärendil are among the least developed in the Legendarium, despite their central importance.
The most important references are HoME IV which includes the Ambarkanta. and the Eärendil passages would probably make sense in the light of this text. The others are in HoME X Morgoth's Ring, which has a whole section about the major cosmological changes that Tolkien was intending to make.
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I prefer history, true or feigned.
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