Try triggering on the key release instead of the key hold. I’ve noticed that effects sometimes do weird things (especially on older Inovelli firmware) when button states change. For example, they’ll sometimes get cleared if you turn the light on or off while the effect is running. You might be hitting an issue with the effect starting while the key release happens. Try holding the button until after the effect clears and see if the behavior changes. If it’s still not timing out after 6sec, that’s curious. If the effect times out correctly when you hold the button until it ends, then update to the latest firmware.
My script (shameless plug) works differently than Brian’s, as I recall. The last time I looked that was using the bulk parameter for effects, which changed a bit in the latest Z-Wave JS update. I don’t think that’s the problem, but it’s something to look into (since you’re not getting any other responses).
I do something similar with locks to prevent lights from turning off which are triggered by the config button, but I’m setting the LED color and leaving it, instead of using an effect with a timer. If you don’t figure this out, I’ll play around with it a bit this weekend and make my locks behave like your alarm notice. I’m curious to understand the behavior.