As you have observed, an event instance cannot normally perform a transition while already in a transition timeline. If you want to achieve the behaviour you describe, there are a few different ways to do it.
Playing the ending sound in a separate event, as you suggest, would be a simple and effective solution.
Another possibility is to remove the transition timeline and change the instruments at the end of the loop from synchronous to asynchronous mode. Asychhronous instruments will be able to continue playing even after the the loop occurs, ensuring that their final notes play over the start of the loop whenever a loop occurs; and removing the transition timeline will mean that ther’es nothing stopping the transitio nto end from occurring.
Without knowing more about your requirements, I can’t say which of these options is better suited to your project. I therefore recommend you experiment with them and find what works best for you.