Simple.
Because the Freescale Coldfire processor family is not completely compatible with the 68000.
Many instructions and addressing modes are not present are other operate differently then they do on the 68K.
These differences require software traps that limit the efficiency of the Coldfire while it tries to emulate a 68K.
That's why the Natami uses a real 68060 or an FPGA emulated 68K CPU.
Does anyone know? Have the Atari guys figured out how to make an efficient emulator, or are they taking the performance hit? Or does the Atari use fewer of the 68K instructions that aren't a part of the ColdFire?
(Serious questions - I know close to zero about the Atari)