Problem 1: driver doesn't detect card removal. On Pi2 the card detect pin on the controller was actually wired up to something, and so the ArasanMmcHostDxe (presumably, written by MS) worked as expected. On Pi3 that card detect pin on the controller always reports a present card.
Problem 2: driver doesn't detect card (re)insertion. Because the driver doesn't detect a card being removed, the SD card and host are not reinitialized, so the card doesn't work.
Problem 1: driver doesn't detect card removal. On Pi2 the card detect pin on the controller was actually wired up to something, and so the ArasanMmcHostDxe (presumably, written by MS) worked as expected. On Pi3 that card detect pin on the controller always reports a present card.
Problem 2: driver doesn't detect card (re)insertion. Because the driver doesn't detect a card being removed, the SD card and host are not reinitialized, so the card doesn't work.