To answer your claim. If questions arose in the past when the Holy See had control over the masses those very same persons would be put to death, only just because, I do not comprehend the logic side of the Bible.
Before excepting as a truth (faith I presume) one must question before excepting and make a deduction in order to arrive at some acceptable and honourable conclusion otherwise we just take for granted the outcome.
So it is good on your part that you have questions in regards to Philosophical sides so you can make your own assumption. It seems though that you accept the writings of man that hath written the Bible without even questioning wether there is a logic or a truth/s just because conditions won't allow you to reflect and those very conditions are chains that tie you down to your own beliefs. I've got nothing wrong with that as my opinion remains mine and I'm not here trying to sell you anything. Just accept that in Philosophy we don't use blind faith or a stealth God/s