missing tool

I think you're trolling.

can't check if the board itself is correct (mem access, instruction set, timing ...)

The functions you mention are withing the atmel chip, not "board level." Contact Atmel to see if they have a chip diagnostic. Don't expect them to fit on the chip at the same time as any reasonable application, though.
Also review their policy about the use of their products in "critical" applications, which is probably similar to that of every other component on the board. Don't worry, if your Arduino-based autonomous drone crashes on someone's head, I'm pretty sure that pretty much everyone in the purchase chain will get sued, in the hopes that one of them will have enough money to make it worthwhile.