After a few nights of debugging and a missing "okay" progress has been made to land in rootfs and make this board usable under Linux.
The journey started with the initial limitations of how the at91sam9260 was used 15 years ago. The uP doesn't have support for SDCard boot and that's why the SPI flash is present. The NAND storage was dismissed as the board area wasn't enough for another big IC and microSD cards are more versatile.
Atmel (Microchip nowadays) has a weird boot mode where the chain looks like this. First the embedded BootROM loads AT91Bootstrap from flash, which loads UBoot which in its turn loads the Kernel and DTS for this board.
The custom part is that i wanted to load the Kernel and rootfs from SDCard (if present) otherwise drop to a compressed rootfs and kernel in flash (as recovery mode).
Right now i have solved the AT91Bootstrap, my fork with glasnost_mk2 target is here.
U-boot with a modified DTS (found here) is able to detect the SPI flash and SDCard and load a mainline kernel.
The Kernel boots and detects the rootfs but hangs at init step.
I need to fiddle a bit more with the BusyBox rootfs in order to finish the bringup.