Why can toggling a variable trigger audio on hidden layers?

This is certainly unexpected behavior. However, it suggests that audio in Storyline is not strictly tied to a specific layer, slide, or even a slide property. Instead, Storyline seems to manage audio files separately, storing them in a content folder within the project. This means that audio can play independently of the layer or slide it is associated with, depending on how it's triggered or toggled.

In your example, the audio is triggered based on the value of a variable and is technically played directly from its source, rather than from the layer where it resides. For instance, on a blank slide, the same audio can be played directly from its source using JavaScript, even if it's not added to the slide itself, whereas media triggers typically only control audio files assigned to specific layers.
Whether it's a bug or not, you’ve certainly discovered something that could be advantageous to others.

However, I experimented with your file and managed to stop the audio from playing on the other layer when a button is clicked on the base layer. Although this workaround addresses the issue, I’m not certain it will help you achieve the more complex functionality you initially intended.