Had a conversation with Intel a few minutes ago. Here is the deal:
The SATA 2 and SATA 3 logic cores on the PCH are separate. When the SATA 3 logic detects a SATA 2 device, it runs in compatibility mode WITHOUT switching back to the SATA 2 logic.
This means the SATA 3 transistors when running in SATA 2 mode is COMPLETELY SEPARATE from any issues.
The reason I assumed this is because other controllers like Marvell default legacy commands through the standard SATA 2 channels. If Intel had done this, then ALL ports would have been affected.
So....I stand corrected. Happily I might add.