Hi:
I can answer part of your question:
1) Yes, you use the rbf file, this is the "Raw Binary Format"
2) When the Stratix device shifts in, it's expected the data to be shifted LSB first, but the EPCS shifts MSB first, so this is the reason for the byte reversal. I don't know if the altasmi_parallel handles this for you or not.
3) The RBF is an optional output format that is available when you build compile your design. Under the "Assignment" menu in Quartus, click on Device->Device and Pin Options->Programming Files then make sure there is a check mark next to Raw Binary File (.rbf)
Hope this helps
Pete