GhstWlf: Correct, the base model offers those two frequencies. The overclocking options add more frequencies, keeping the slower clock rates available.
As for speed and performance of the "seemingly same" processor, you should know that real fastmem just beats the crap out of Chipram, giving the same processor a substantial performance boost. A very simple rule of computers applies here, one that will always remain true: A processor can only be as fast as the memory where the instructions come from.
Also, the ACA1221 sports a full 68020 processor, not the 68EC020. This gives it the possibility to access more than 16MBytes of address space. If you only add fastmem to an A1200, you'll max it out at around 10MBytes. The ACA1221 on the other hand can give you a total of 63MBytes of memory.
Check out the benchmarks here: http://wiki.icomp.de/wiki/ACA1221#ACA_12xx_Benchmarks