Depth in timeline

You can use the layer and position your element twice on the timeline and use the display property to hide one and show the other.

You could also create a function in Hype on scene init:

hypeDocument.setDepthOnElement = function(depth, selector) {
    var sceneElm = document.querySelector('#'+this.documentId()+' > .HYPE_scene[style*="block"]');
    var elm = sceneElm.querySelector(selector);
    this.setElementProperty(elm, 'z-index', depth);
}

Now use this in your head:

From here on out you should be able to use timeline commands triggering a custom behavior that looks something like this:

setDepthOnElement | 1 , ".myRedSquare"

Code is untested as I am on the road and only have access to my iPhone. Should work.