The WiFi/BT in the Librem 5 is using SDIO and I2S, but there are also two lines (USB2_WIFI_DP and USB2_WIFI_DN) between the USB2642 and M.2 slot for the WiFi/BT card. Maybe those two USB lines aren’t used, but I assume that Purism connected them for some reason. Maybe Purism is keeping the possibility open for future WiFi/BT cards that need USB, or maybe Purism thinks that people will want to use other types of cards.
Since the USB2642 contains a USB hub, I wonder if Purism could have found a similar chip that supports USB 3.0 to allow high speed access to the microSD card, and then run its USB hub at USB 2.0 speed to connect to the cellular modem.