What Installation Master are you using to conduct the System Copy? In case of CE since it is based on AS JAVA and anything with AS JAVA Export & Import is always used. Since you are first choosing the source system (AIX) and after the export the target system (Linux), the Installation Master automatically knows that it is a heterogenous process. It has been a while since I last migrated AS JAVA systems but unless I'm mistaken, a migration key is not required for AS JAVA, only AS ABAP. I do however wonder why you haven't seen the screen where the Installation Master asks you to confirm the endianess. Maybe you have chosen wrong source or target options or you are using the wrong Installation Master.
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