I am currently talking to our JTAG provider concerning the JAM file created from the JIC, looks promising at this stage.
--- Quote Start ---
Just be sure to create and use two JAM files, one that flashes the SFL image into the FPGA and one that uses it to put the design into the flash memory.
--- Quote End ---
I tried this out using a standard ByteBlaster but what happens is that after the SFL is loaded in the FPGA when you program the final image it is just overwriting the SFL in the FPGA's SRAM i.e. not going through the SFL. Therefore as you mentioned earlier I am fairly sure you have to use the auto detect and attach a JIC file to use the pre-loaded SFL.