Right, nested parallel branches are supposed to look flattened, thats what DAG is returned by nodes API. That part looks fine. Tried on latest master, stages/parallels appear fine in karaoke(as build progresses). Probably whats reported is probably fixed in https://issues.jenkins-ci.org/browse/JENKINS-39229.
vlatombe As mentioned above, I suspect you are not seeing node graph only in initial run, on page refresh or if you clikc on previous run, you should see the node graph as below.