I'm not sure, but do you realize that it's the same word twice (Theos)? It's merely inflected differently because of the two distinct grammatical usages. It is normal that when we refer generically to a greek word that we tend to refer to it using the nominative case, which is why in english we would tend to just say we're talking about the word "theos". "Ton" is the article and is also simply presented in the same case as the noun that it's modifying.
Θεός (Theos) - 2nd declension nominative (the subject of a clause)
Θεόν (Theon) - 2nd declension accusative (the direct object of a clause)
See for example
Appendix:Ancient Greek second declension - Wiktionary
Or, for another example, It's still the same word in verse 6 which says Ἐγένετο ἄνθρωπος ἀπεσταλμένος παρὰ Θεοῦ ("There was a man sent from God"), where it's now in the genitive case (Θεοῦ) because that's the normal case used for an object of the preposition "from" (παρα). Or in John 9:24 when the religious leaders are questioning the man healed of blindness, and say that he should give glory "to God" (Δὸς δόξαν τῷ Θεῷ). Here Theos is in the dative case, as the object of the preposition "to". It's all the same word, and the way the root changes based on the grammatical case does not reflect any particular semantic difference as far as there being "two different Gods". Not as a matter of grammar. Note also that it's not a question of the presence or absence of the article determining the semantic meaning either, since you will agree 1:6 is not referring to Jesus or the Logos but to the Father, and does not include the article. "para theou" and not "para tou theou".