This is my understanding about the actual specifications:
SATA (v 1.0) provides the PATA command queuing. It should therefore pass through, but again, I will need to read the spec again. No Native Command queuing (It is not listed in the 1.0/1.0a spec command layer)
[This paper is long, but a reading of the outline, and a search of the text did not reveal any instances of Native Command Queuing]
SATA II (v 1.1) provides Native Command Queuing. ( 1.1 spec Section 4 - Command Layer). It is very clear and prominent in the paper.
So, the Raptor would be hardware compatible with SATA I command queuing (which is really PATA), and SATA II give us what was advertised - Native command queuing.
Which would also mean, that the Seagate drives will migrate nicely to SATA II controllers, while the Raptors would be permantly mated to a PATA Command queuing SATA controller [whew!], If that feature was needed.
If the Raptors actually support "Native Command Queuing" then they are ready for SATA II.
Any of this could be implemented in the drivers or firmware, I would suppose.
Also, I do not know if SATA II supports the older PATA Queuing.
For people buying the new raptors just for command queuing, they may not get what they want.