You get the same Read/Write performance if you connect the HDDs to the Intel or the 3rd party (ASMedia, Marvell) SATA ports.
No HDD can spin fast enough to saturate a SATA 2 (3Gb/s) port, let alone a SATA 3 (6Gb/s) port.
It's when you are connecting SSDs when it makes a difference. The 3rd party controllers were developed when 1st generation SSDs were made. They can't handle the speeds of current generation SSDs. If you connect a current generation SSD to a 3rd party port it will get SATA 3 speeds, but it won't get maximum advertised SATA 3 speeds.
If you need to connect more than 8 HDDs then yes, add a PCIe card (minimum x2) for additional ports.