I'm looking in to your question now. This is what I found so far. It is not yet a complete answer, but it is far too long for a comment, so here it is.
The physical SD card slot on the Raspberry Pi is connected to GPIO pins 48 to 53. I dumped the status of these GPIO pins and determined that in normal use, these GPIOs are set to ALT3. The functions of these pins are completely undocumented.
The device tree overlay switches the function of these pins to ALT0, which is also undocumented. It also switches pins 22 to 27 to ALT3, which is documented as being SD1.
Now from the forum thread we read this:
SDIO is supported by the mmc (SD1) driver. In order to use SD1 for SDIO, you'll need to use SD0 (sdhost) for booting, as SD1 is currently being used for this. Phil has written a device tree overlay which does this.
Based on this we can infer that the default function ALT3 on GPIO 48-53 (card slot) connects those pins to SD1 (eMMC). ALT0 connects those pins to SD0 (sdhost). This frees up SD1 to be connected to GPIO 22-27 for SDIO purposes. Interestingly, GPIO 22-27 has an undocumented ALT0 function. Perhaps this connects those pins to SD0 (sdhost)?
Now the detect pin. According to the available schematics, card detect is on GPIO 47. This GPIO is not altered by the overlay, which means it will still presumably deliver any input to SD1, which is now controlling your SDIO card, as long as you have a microSD card inserted as well. So SD1 should still think there is a card inserted, because there is.
This raises the question of how SD0, now controlling the card slot, is able to detect the card. Since you are still able to boot, this suggests that the card detect signal is not really very important to the functioning of the system.
Further evidence for this comes from my dump. In normal use, this pin is set as an output, which means it isn't actually going to do anything. It is possible that the state may change if I eject the micro SD card. I can't really test that for obvious reasons.
A little more reading of the device trees and it turns out GPIO 47 is also the GPIO which controls the SD card activity LED, which explains why it's normally an output.