Update: Thinking about it some more, I think Pieter is right and there is little harm in merging the list of enumeration values. I have already implemented this in our code bases and future versions of Mendix 3 and 4 will merge enumerations without conflicts!
Old answer: If two people both add a value to an enumeration in separate branches, then there will be a conflict on the enumeration. We decided not to merge lists of enumeration values because their order is important. You can resolve the conflict by choosing one of the alternatives. Afterwards, you will have to add the missing value to the enumeration. I do not see how microflow calls are impacted by this.