The Mojo uses the "Slave SelectMAP" interface to program the FPGA (see https://www.xilinx.com/support/document ... app502.pdf). The Mojo doesn't actually connect the flash directly to the FPGA but through the microcontroller. The microcontroller reads the contents and programs the FPGA.
The easiest way to achieve Mojo compatibility is to use your ATmega1280 to do the programming and flash management. As long as you make your firmware work the same as ours (https://github.com/embmicro/mojo-arduino) and you use a serial interface to your computer the IDE should work fine.
General discussion about the Mojo