Focus Order, Accessibility, and Set Focus

That's what I thought, that Set Focus only triggered yellow squares if the objects were interactive.

However, you click the button to trigger the layer, and the button itself gets the yellow square UNTIL the set focus kicks in and moves it to the right object

I found that NVDA read things automatically if elements in the screen reader appeared at 0:00 in the timeline, so everything fades in after 0.25 or after the appropriate animation occurs.

So, in this case, since I used "Set Focus on Title when Timeline starts on Title", the yellow box appears on the previous element that triggers the layer until it is visible.

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To answer your second question:

If I keep the "Prevent Users from Clicking on other layers" checked/enabled, and 0 set focus, the screen reader loses focus in the slide and gets kicked out to player controls and needs to find the back to top button.

If I don't keep "Prevent users on clicking on other layers" checked and disable it, this seems to solve the issue. Pressing down will work.
--the Downside to this if there are several layers and you are in deep and cycle through back to top, you have to start all over from the base slide and navigate through the focus order, which could be annoying for those users and cause frustration.