I think the main problem could be not realizing the following.
Let us take one sensory faculty: cakkhu.
In “Cakkhuñca paṭicca rūpe ca uppajjati cakkhuviññāṇaṁ,” cakkhu does not mean “physical eyes,” “rupa” does not mean “physical rupa (say a tree),” and “cakkhu viññāṇa” is not a “pure seeing event (seeing the tree).”
- That contact occurs in the manomaya kaya, with the cakkhu pasada rupa (carrying an IMPRINT of the tree) hitting the hadaya vatthu. Thus, “rupa” here is not the tree! Cakkhu is not physical eyes, even though they play a role.
- That gives rise to a citta, which CONTAMINATES within the lifetime of that citta to viññāṇa. That is the first stage of contamination. The second stage of contamination takes place in the next step, “Tiṇṇaṁ saṅgati phasso.” See “Loka Sutta (SN 12.44).”
- That holds for all six sensory contacts.
- So, cakkhu already became an āyatana at the very beginning. Even if the mind may not attach to that particular ārammana, the mind goes through the “nine stages of contamination.” See “Citta, Manō, Viññāna – Nine Stages of a Thought.”
- P.S. In the same way as the cakkhu indriya automatically becomes cakkhāyatana, mana indriya automatically becomes manāyatana.
- Thus, all six sensory faculties are generally āyatana unless one is an Arahant.
Details at “The Five Aggregates (Pañcakkhandha)“
