I haven't tried it, but I don't believe it will work. The commands are the same however, what is not specified is the carriage returns and line feeds - so I do not know for sure if they are the same.
For sure the block erase won't work, the high speed comms option won't work (not supported in the Atmel device), reading part of the signature, HSB and bootloader version are not supported.
If you try and use Flash Magic there is no guarantee that you device will be left in a state where you will be able to reprogram it. So I suggest you stick with FLIP from Atmel.

Andy
Embedded Systems Academy
aayre@esacademy.com