What do you mean by "the data transmission speed" ?
When the firmware is programmed into the EEPROM, the firmware will be downloaded from the EEPROM
into the internal RAM. So, the transmission speed of the USB transfer handled by the firmware are equivalent.
The transmission speed to program the EEPROM is slower than RAM's one because the EEPROM takes so long time than RAM.
When the firmware is downloaded into the EEPROM, FX3 receives the firmware data over USB and then transfers it to EEPROM over the I2C interface which runs at 100kHz/400kHz. In case of downloading firmware to RAM, the firmware data is transferred into the FX3 SRAM over the USB interface, which operates at a data rate of 480Mbps.