What's the purpose of specifying SPI CE0 and CE1 when you can just toggle regular GPIO?
The difference is that the Pi's SPI hardware will automatically assert and deassert those GPIO as needed.
As you suggest this isn't a great benefit and in fact the current Raspberry Pi Linux SPI driver does toggle the slave select GPIO itself rather than letting the hardware do so. It does this so you can more easily add additional slave select GPIO.
If you have more slaves than are supported by the SPI drivers you have no choice but to toggle the GPIO yourself.