A bit of research lead me to this. The SYSCFG0 fuse byte is supposed to be 0xC9 (according to the datasheet), not 0xCD like the fuses_4809.bin file specifies.

I can see you've done an attempt in the boards.txt file, but this line is not picked up by avrdude.

But why bother with a binary file in the first place? Each fuse byte is accessable by passing fuse0..fuse8 to avrdude ("-Ufuse5:w:{bootloader.SYSCFG0}:m" for instance), and it makes everything more transparent to the users and developers. I actually had to find myself a binary file editor in order to track this down.