These were in linker script "flash_with_bootloader.ld"
MEMORY
{
FLASH_FPGA (r) : ORIGIN = 0x00040000, LENGTH = 0x00200000
FLASH (rx) : ORIGIN = 0x00000000+0x2000, LENGTH = 0x00040000-0x2000 /* First 8KB used by bootloader */
RAM (rwx) : ORIGIN = 0x20000000, LENGTH = 0x00008000
}
.fpga_bitstream_section :
{
KEEP(*(.fpga_bitstream_signature))
KEEP(*(.fpga_bitstream))
} > FLASH_FPGA
Didn't find bootleader sources. This atleas put FPGA image outside of SAMD flash area so bootloader should detect this and write it to FPGA FLASH.