So it is possible to easily for the FX3 to switch to silicon bootloader mode. This is useful for experimenting with different firmware without touching the SPI and also without the need for JTAG. I found this out when trying to connect a 3.3v UART cable which is not an good idea since all I/O on board are 1.8v. Basically UART TX/RX are multiplexed with SPI MISO/MOSI, but thankfully it didn't fry the SPI flash which is 1.8v. However it led the board to start in DFU mode.
So to replicate this behaviour it is enough to connect a 1.8v pull-up (here's I'm using a 2.2K) to MISO. Then the board will start in bootloader mode (device/product ID 04b4:00f3).