The root cause of JRA-16465 was that the transition created in JIRA fired Generic Event instead of Issue Updated event.

When you're adding a new transition, I think it makes sense to default the event fired to Issue Updated rather than Generic Event. It's pretty typical that a project will have a notification scheme where some users will be notified when an issue changes, and this will mean that these users will still be notified when the new custom transition is used.

With the current behaviour, you're likely to leave the Generic Event in place on the transition, and have the notification scheme configured such that noone is notified when a Generic Event occurs. In this case, nobody in the project will get notified about any use of the new transition on issues in that project.