Strange that none of the Atmel data sheets are available. It is only available with 324 pins which suggests a BGA package, can you handle that?
As for reliability, I would take it for granted they are equally reliable, similar testing would be done on each family of devices and even over a production run, any problems would be fixed with a new silicon revision.
I wonder why you need such high speed for servo control, CNC is generally quite slow compared to the processing speeds of MCUs.
Although I can't be specific without the Atmel data sheet, the things to watch out for are:
1. The 'throughput' of a processor is related to the instruction execution speed, not the clock speed. A fast clock that needs many cycles to process each instruction may be slower than one with a low speed clock that performs one instruction per cycle.
2. How much additional interfacing is needed. For CNC work for example, you might have use of on-board quadrature decoders, some processors have them, some don't,
3. Is the supply voltage and hence output pin voltages able to drive peripherals without additional external level shifters.
4. What other peripherals does it need to communicate with other devices? (serial, USB, Ethernet, SPI...)
5. As mentioned earlier, can you or your board assembler handle BGA devices or are you better staying with pinned/legged devices.
Brian.