I originally posted this question to an existing thread since I ran into the same problem that had been apparently been solved, but the solution actually only improves the situation and additional enhancements may be needed. However, maybe it's appropriate for a new thread of its own:
As shown in the attached diagram below, we have observed that when a process is created in Eclipse, and then deployed to a Runtime engine, the positioning of the sequence lines is not exported correctly to the bpmn file. As a result, any diagrams generated by calling the Activiti APIs is slightly different from the Eclipse version, and depending on the complexity of the diagram, they may or may not have significant impact on readibility.
The example I am posting below is relatively simple, created solely to highlight the types of variations in sequence line positioning. Kindly advise if this is something that is planned to be addressed soon:
But I don't know if they would solve the issue you are highlighting. If it is important to you, please file a Jira with the bpmn 20 xml so we can verify the exact problem.