The controller and drives still communicate with each other via SATA and the speed is the same.
However, the BIOS controls how the SATA controller presents itself to the OS - as a native SATA controller (AHCI mode) or as an IDE controller. What some BIOSes call "IDE mode" is referred to as simply "compatibility mode" in others.
The main difference is that in IDE mode, the OS can't take advantage of native command queueing (NCQ) or hotplugging drives, since these are not features that a real IDE controller would know about. The SATA controller and the drives still understand these features of course, they simply aren't used in IDE mode.
I tried running my system in AHCI mode and also saw no noticeable improvement from it - but the biggest annoyance for me personally was that I was now stuck with the Safely remove hardware
icon (because of hotplugging capability). To me that says "I left an USB stick/external HD plugged in" so it really irritated me...well, back to IDE I went