I'm not 100% sure why they do that, but my guess is to increase the number of SATA ports beyond the northbridge's capabilities. I would use the Intel controller (yellow), personally, as they tend to have better overall performance.
the 6 yellow ports are pulled out from the Intel Z87 PCH (Platform Controller Hub). These ports are fully AHCI and SATA-III compliant .
The 2 brown ports above are pulled out from an ASMedia 1061 SATA controller. The 1061 is connected via PCIe 2.0 lanes pulled out from the PCH. These ports should only be used once all 6 yellow ports are full and can only be used for hard drives