Hardware

PCI-E is on the periphery of the circuitry, hanging off the edge of the motherboard, whereas the on-board controller is closer to the bus.

What you also have to take into account (but haven't mentioned as yet..) is the read/write speeds and the rotational speeds of the hard drives in question - the SATA is only (as it was touted at its launch "a wire replacement for an old serial connector") capable of up to 3Gb [Gigabits], not 3GB [Gigabytes].

If as you say, the progress bar was "all over the place", I'd be tempted to inquire what else the system was doing simultaneously since clearly the system-estimated duration kept adjusting to some sort of change in cycle priority.

*I think THIS rather sums up what I was trying to blurt out in my usual Scottish brogue:

For mechanical hard drives, SATA 3 Gbit/s transfer rate is expected to satisfy drive throughput requirements for some time, as the fastest mechanical drives barely saturate a SATA 1.5 Gbit/s link. A SATA data cable rated for 1.5 Gbit/s will handle current mechanical drives without any loss of sustained and burst data transfer performance. However, high-performance flash drives are approaching SATA 3 Gbit/s transfer rate.

Excerpt from:
http://en.wikipedia.org/wiki/SATA

In other words, just because you've got a 3Gb interface, doesn't mean you've got that capability in your hard drives.

..wait for TheChas to come along and **** me right out of the water.


Edit for *

I repeated the tests - this the transfer speeds were only a shade quicker on the onboard SATA (2 mins 55) than PCIe SATA (3 minutes).

I guess I've got my answer then: PCIe can be about the same (at best), but can also be much worse...

Cheers,

Richard


PS - Did you like the name 'MacSedroom'?