I managed to replicate the described issue. However, the AppBar is not part of the Hybrid UI components, thus such behavior is expected. Please note also that when using Hybrid components we recommend using the LESS themes.
In the current scenario, I would suggest you use a different position mode for the AppBar positionMode, for example, if it is suitable for your scenario, you could set it to "fixed". Or if you decide to use the "sticky" positionMode, you could try some of the approaches suggested in StackOverflow for setting fade-in transition to sticky element.
In order to resolve the second issue with the disappearing red 'div', I would suggest you set the height to the "view 3".
<script id="view3" type="text/template">
<div style="width: 95vw; height: 800px; background-color: beige;">
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