What did you connect the second USB port to on the E Series module? The u-blox USB port pins? That definitely will not work. That’s directly connected to the modem and is not accessible to user firmware.
The SDFAT library is meant to use an SPI-connected SD card adapter. It will definitely not work with a USB connected one, on any USB port. That would require a USB host mode and a device driver for the SD card. Neither exist and would be exceptionally difficult to implement. For all practical purposes, impossible.