More likely the use of 3 Color Codes is to allow more flexibility on the repeaters. Like Transportation has one color code for Bus/Garage ops, Administration has one, and Security/Maintenance has one. And with three CCs, 2 Slots, and multiple TGs, you can turn 2 repeaters into basically a small TRS without adding the cost of going to an MotoTRBO TRS... Though you also don't get the added features a TRS would give. Advantages, and disadvantages to being cheap...
2 Repeaters... 3 CC... 2 Slots... That is 12 possible chans alone... Add in multiple TGs... That is pretty big small system. Then you have the direct/talk around options...
Same way that using multiple CTCSS/CDCSS tones works on analog multi user repeaters to an point.