I can give you a good example of why you might want to use the SPI flash. You can get the FPGA up and running in milliseconds. We were running a Microblaze with a Linux kernel and the FPGA could perform its functions autonomously once Linux booted. If you program from the Pi or BB, you have to wait for the Arm Linux to boot before your FPGA can begin loading. It really just depends on what your design goals are.
Received! I got the full package (Edu/Cam/Bone/Pi). One thing I noticed..... seems built in Shenzen (20 min from Hong Kong), but then shipped to Singapore... and then shipped to US. My wife was literally minutes away from just picking it up in person. Oh well. looking forward to trying it out after I solve some work emergencies.