I think it should be quite common question.
Based on my own experiments, if the order of the element in unordered list is different in the two compared model even if the content of element are completely equal.
I think it may be the default behavior of EMF Compare.
I'm wondering how can I override this behavior?
Is it very hard to implement?
It seems your question is relative to EMF Compare, not EMF Diff/Merge.
The former is a full end-user solution, the latter is an engine for building tools that manipulate models by merge (although it provides a sample GUI).
I see that you have also posted on the EMF Compare forum so I guess it's fine.