I just wanted to post some testing results I have completed using my main FreeNAS machine (the Asus/AMD one).
I loaded the FreeNAS-9.3-BETA-201412060221 image and it seems to work fine. There were no USB Flash drive issues, is all booted fine, rebooted three times during the update and twice after I loaded my config file. I did not do a direct upgrade from 9.2.1.x to 9.3-Beta. My only issue that I have noticed so far is the MiniDLNA plugin that I manually installed no longer works. I'll have to look into this more but it's not a deal breaker for me.
EDIT: Boot times are normal using the USB Flash drive.