No, the GPIOs are not connected directly to the endpoints. The actual architecture is similar to FX3 which you can read about in Chapter 3 of the FX3 Programmer's Manual.
If you want to do transfers, then using GPIOs is not recommended. It will be very very slow and will involve a lot of code. You can instead use GPIF (for which you need FX3S). Otherwise, you can use SPI, I2C, UART or one of the SD ports.