040 is the cpu, it's independent of the model name. It's not ideal to reconfigure exact computer models for processor intensive tasks. None of the games you mentioned are designed to run well on a plain amiga 1200 for example. Just use 040, it'll be like using 486 instead of 286
Not identically of course but I mean you'll be just telling the emulator to use a faster cpu, regardless of the model of the amiga you think you are emulating.
JIT is something I can briefly explain as: Not good for retrogaming or compatibility but ideal for situations performance is important. Your problem is the 020 there. Try not to use JIT, if it still runs bad with 040, which alien breed shouldn't but doom might, then turn on jit and add some cache to it.