The permissibility of naming after the Prophets, and reports disliking it

Abu Bakr bin Muhammad bin Amr bin Hazm narrates from his father that Sayyiduna Umar bin al-Khattab (may Allah be pleased with him) gathered all the boys whose names were the name of a prophet, then put them into a house and firmly resolved to change their names. Then their parents testified: "Indeed, the Messenger of Allah (peace and blessings be upon him) himself gave them these names." The narrator says: My father, Muhammad bin Amr bin Hazm, was also among those children.
The chain of this hadith is hasan (good).

It is narrated from Sayyiduna Anas (may Allah be pleased with him) that the Prophet (peace and blessings be upon him) said: "You name them (the children) Muhammad (for the blessing of my name), but then (in a state of slight annoyance or anger) you make them the target of curses and reproach."
Imam al-Tayalisi narrated this hadith through al-Hakam bin Atiyyah from Thabit; and Imam Abu Ya'la recorded the same text through Abu Musa and Abu Dawud al-Tayalisi, and Imam Abd bin Humayd through Abu al-Walid and al-Hakam bin Atiyyah.

Al-Nadr bin Shufayy narrates it from the Prophet (peace and blessings be upon him) as a marfu' report, that he (peace and blessings be upon him) said: "Whoever has three sons born to him and does not name even one of them Muhammad (with the intention of seeking blessing), he has certainly shown ignorance and deprivation."
Imam al-Harith recorded this hadith in his Musnad; however, because al-Nadr bin Shufayy is majhul (unknown) and because of the weakness of Isma'il bin Ayyash in his narration from non-Syrians, this report is extremely weak and unreliable in terms of its chain.

It is narrated from Isa bin Talhah that the wet nurse (foster mother) of Muhammad bin Talhah told him that when Muhammad bin Talhah (may Allah be pleased with him) was born, we brought him into the blessed presence of the Prophet (peace and blessings be upon him). He (peace and blessings be upon him) asked: "What have you named him?" We said: "Muhammad." So he (peace and blessings be upon him) said: "This is my name, and his kunyah is Abu al-Qasim."
The narrator Ibrahim bin Uthman bin Abi Shaybah in its chain is weak, because of which this chain is weak; however, Muhammad bin Talhah's being named after the Prophet (peace and blessings be upon him) and his being given the kunyah Abu al-Qasim are also established by other historical reports.