The order is determined by the order of the scenes in XML (right click → open as .. → source code) under the node scenes.

Note that on this XML, the “Splash” scene starts first, followed by two navigation controllers, and this is what is shown on a regular storyboard.
<scenes>
<scene sceneID="tne-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
<scene sceneID="ane-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
<scene sceneID="bne-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
</scenes>

Here, however, I moved the node scene for a splash under the navigation controllers, and it updated the storyboard view accordingly.
<scenes>
<scene sceneID="ane-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
<scene sceneID="bne-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
<scene sceneID="tne-QT-ifu">
<objects>
</objects>
<point key="canvasLocation" x="-876" y="-1364"/>
</scene>
</scenes>

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