Perhaps, but the PCI card also contains it's own controller instead of using the existing SATA controller in the box. Not a complete justification for the added cost, but even if the flash is the same, getting it connected is more hardware than a SATA device needs.

Ultimately it doesn't matter why the performance is higher. Also, the Intel 750 has 18 channels while most SATA SSDs have 8-10 channels.