Yes, device is configured for active serial. The officially supported flow is that you include a library in the Arduino ide and that will link a ttf file at the end of the Sam application, along with an header carrying destination location and checksum. If you want to burn your image then you need to create your own header file including your ttf and go through a script that creates the header. I'll try to post instructions on this shortly.
Configuration at boot is very fast as fpga loads from flash at around 40 MHz if I'm not wrong and bitstream is around 300kbyte. The only caveat is that we go through two bitstreams now. The first is automatically loaded and the second is loaded after Sam boots and issues the load command to the fpga. If you want to avoid this you can replace the boot image with your customer one.