The reasons for caution with the SPI pins are two-fold:
- the flash chip containing the firmware and user files is connected via these pins. If you use them in an improper way, it will likely affect access to the file system, crash the system or prevent it to boot, and if write operations are disturbed, also brick the Omega as a worst case. But as long as your external SPI device properly behaves and is off the bus when CS1 is not active, no problem here.
- In addition, the three SPI output pins (MOSI, SCK and CS1) also serve as CHIP_MODE inputs. This means right after reset or powerup, the logic level on these pins is sampled to configure how the chip starts up. To make these levels as needed at startup, the Omega2 has internal pullup and pulldown resistors on these pins. Now, if you connect something to these pins that has a lower impedance than those resistors, the CHIP_MODE will be wrong and the Omega will not start correctly. Again - a properly connected SPI chip should have high impedance MOSI, SCK and CS1 inputs, and will not disturb operation. But for example if you connected a LED to CS1 to see when your external device is selected, that would be a lower impedance and might change the CHIP_MODE at startup.
Note that there are more MODE pins that may not connect to anything of low impedance during startup for the same reason: GPIO1 (DRAM_TYPE), GPIO45/TX1 (JTAG_MODE) and GPIO12 (EXT_BGCK), and some more on the Omega2S.
That's why I marked them bright red on my extended pinout diagrams - it's too easy to forget about this when looking for a free GPIO otherwise ;-)