You said, “In the Bhagavatam verse that mentions our origin, in 4.28.53-55, Krishna twice says that we rejected Him and came to this world, that it was our choice.”
Sri Visvanatha Cakravarti Thakura states that this leaving is from Maha-Visnu after the mahapralaya.
1. The assumption is that 4.28.54 retroactively applies to 4.28.53. The soul can reject Krishna and come to this world, and then remain without a home during the Maha-pralaya. I don’t see evidence that these two events are necessarily simultaneous.
2. In fact, the soul does not “reject” the Lord, when coming out of His body to reappear in the material world. Rather the Vedas state that the Lord sends them into the world. All the descriptions we have in Shastra of this event indicate a passive role for the Jiva of being sent back into the world, and not an active role of rejecting the Lord.
3. While we revere VCT, our system is guru, sadhu, and Shastra, and so he is not an independent authority. Prabhupada often said that we are “originally Krishna conscious.” He named his magazine BACK to Godhead, and BACK to Godhead was the theme of his mission. To be unconscious and inert in the body of Mahavishnu is not exactly to be in loving Krishna consciousness, and does not explain Prabhupada’s claim that we are originally Krishna conscious.
4. Krishna asks the soul at 4.28.53 whether he “remembers” the Lord. Since the soul in Maha-vishnu’s body does not have loving friendship with the Lord, remembering that inert condition would hardly count as remembering a loving friendship.