The suttas mention that the "destruction" of the first three fetters is a requirement for stream-winnership. Now "destruction" I take to mean complete annihilation. This just doesn't make any sense to me. How can one not have any doubt at this stage? At best, you could be confident in the teachings, but not absolutely certain. You would think that there could be a translation error here.
It often helps to look at the Pali and/or Sanskrit of the original Pali Canon to gain greater understanding, so I have re-posted the list of fetters, and the Pali and/or Sanskrit for each term.
10 Fetters (samyojana) tying beings to the wheel of existence:
5 Lower Fetters (orambhagiya-samyojana)
1 Narcissism, provincialism, clan identification (sakkaya-ditthi)
2 Skepticism & doubt (vicikiccha)
3 Clinging to rules, rights and rituals (silabbata-paramasa; s. upadana)
4 erotic craving (kama-raga)
5 Ill-will or aversion (vyapada)
5 Higher Fetters (uddhambhagiya-samyojana)
1 Craving for material existence or Lust for form (rupa-raga)
2 Craving for immaterial or formless existence (arupa-raga)
3 Conceit (mana)
4 Restlessness (uddhacca)
5 Ignorance (avija)
Since your question involves the 4 ranks of Noble (Aryan) attainment, then it is also worth reviewing them with respect to the fetters.
1] Sotapanna (stream winner) has eradicated the 1st 3 fetters: Narcissism & clan identification (sakkaya-ditthi), Skeptical doubt (vicikiccha), and Clinging to rules, rights and rituals (silabbata-paramasa); will be enlightened in seven lives or less (cognitive, understanding)
2] Sakadágámi (once returner) has eradicated the 1st 3 & weakened the 4th and 5th fetters: erotic craving (kama-raga) & Ill-will or aversion (vyapada)
3] Anágámi (Non-return) has eradicated the first five fetters
4] Arahatta (enlightened, mystic, one who has attained the deathless) has eradicated all 10 fetters, the 5 lower fetters plus: Craving for material existence (rupa-raga), Craving for immaterial existence (arupa-raga), Conceit (mana), Restlessness (uddhacca), & Ignorance (avija)
(MN 118)
So, the conflict is confusing the 10th fetter, which is ignorance (avija) with the second fetter, which is skepticism & doubt (vicikiccha). Skepticism & doubt (vicikiccha) is really about doubting the spiritual/contemplative life has any value whatsoever. Whereas, Ignorance (avija) is simply not understanding the entire package of enlightenment.
When one enters the stream, as you have done, Michel, one knows that there is more to life than the material existence, and even knows how to make contact with the spiritual dimension. One cannot; however, completely dispel all ignorance (avija) of the spiritual dimension and how the contemplative life transforms one into a whole spiritual being until one is fully enlightened.
The tenth fetter is ignorance. I see that in some of the commentaries and in even some of the sutta translations the term "ignorance" is used interchangeably with "delusion." Do you think that the below reference properly defines the difference between ignorance and delusion?
Considering that Bhikkhu Bodhi's translations are deeply delusional, I would not take his word on any dhamma topic without thoroughly investigating it for myself. After all he is not even a stream winner. He is like most priests of most religions, just someone who put on the robes of office and pretends to be holy and wise, when in fact he has no idea what the dhamma is about.