How can one reconcile the Prophet's (peace and blessings be upon him) dying instruction not to pray over him with an imam after his death, because he is the master of imams, with his prayer behind Abu Bakr Al-Siddiq (may Allah be pleased with him) during his illness?

The Companions prayed upon the Prophet, may Allah bless him and grant him peace, individually and no one led them in prayer. This is a matter of consensus among scholars, though they differed in explaining why. Ibn Kathir mentioned that the absence of an imam was either due to it being an act of worship whose meaning is difficult to comprehend, or so that each individual could directly pray upon him, and the Muslims' prayers upon him would be repeated. As for Al-Suhayli, he said that since Allah and His angels pray upon him, and every believer was commanded to pray upon him, it became obligatory for each individual to do so directly. The mentioned hadith (definition) about the Prophet commanding them to pray upon him individually is weak. There is no issue with the Prophet, may Allah bless him and grant him peace, praying behind Abu Bakr and Abd al-Rahman ibn Awf, as authentic hadiths prove the permissibility of a less virtuous person leading a more virtuous one in prayer.