I understand your hesitation regarding edge-to-edge connections.
BPMN 2.0 is really a big use case for yEd nowadays. Maybe big enough to think again about edge-to-edge connections.
Either "real" edge-to-edge or via a workaround. In the end, it is not edge-to-edge in BPMN. The edge coming from a document links to two different nodes. It is just that the route of the edge should be the same as the sequence route between the nodes (at least for most of the way). Technically, this should be feasible without breaking the graph concept.
Thanks in advance