Does the Prophet's prohibition, upon him be peace, against seeking forgiveness for Abu Talib contradict his attempt to pray over the chief of the hypocrites? And what is the meaning of "the one among you who has collected the most Quran" and "has taken the Quran"?

Allah the Almighty forbade His Messenger and the believers from seeking forgiveness for polytheists, saying: "It is not for the Prophet and those who have believed to ask forgiveness for polytheists, even if they were relatives, after it has become clear to them that they are companions of Hellfire." This verse was revealed after the Prophet, peace and blessings be upon him, said regarding Abu Talib: "By Allah, I will seek forgiveness for you as long as I am not forbidden from doing so." And Muslims used to seek forgiveness for their deceased as well. So the verse became conclusive proof of the prohibition of seeking forgiveness for polytheists.

As for the Prophet's prayer over Abdullah ibn Ubayy, it was based on the outward appearance of his Islam. Then he did not do so after he was forbidden from it.

Regarding burying the deceased in one grave, the meaning of giving precedence to "the one who knows more Qur'an" (أكثرهم قرآنًا) refers to the one who has memorized more of the Qur'an, and this is an indication of his virtue.