nRF9E5 and atmega16
According to the nRF9E5 datasheet, the external boot EEPROM is required. However, after boot is completed, the SPI port connected to the EEPROM is available for other uses. I would think the simplest solution is to connect together the two SPI buses. After the nRF9E5 boots, it should be programmed to place its SPI bus in slave mode. Then after boot, the ATMega16 can be the SPI master and address either the dataflash or the RF transmitter as required.