If the card reader using the SD pins can communicated with an SD card which stores and retrieves data on NAND storage, we should be able to mock out the NAND storage for storage over another protocol (in this case a filesystem accessed over USB). One example is the Realtek RTS5301 used on many USB 3.0 card readers and inexpensive. Let me explain, a USB 3.0 card reader uses a micro controller to read and write to an SD card.
It would have an SD/microSD form factor micro controller + buffer USB 3.0 host computer with modified driver that uses a file as storage (emulated NAND) So how can we do this? The fastest, cheapest, most effective way to do this (theoretically) is to use a hacked USB 3.0 SD card reader. The proposed solution is an sd card emulator.
This is not feasible for an automated system and solution like SD-MUX (multiplexers) still require an SD card and can wear out and require switching which increases complexity. If it works great, if not then we have to re-flash the SD card on the host computer and retry it. During development and testing we flash a bootloader + os image to an SD card on a host computer and then move the card manually to a target device (RPi or similar) and power it on to see if it works. The problem: creating an automated test and benchmark platform for embedded devices, specifically single board computers (SBCs). With that said, I need to emulate an SD card via USB. This might sound crazy but there is good reason for this and carefully considered for over a year from all angles, so if you're comment is "why not try X" without having understood the problem, please do not reply.