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If this is a Drop Down interface tool that you configure in your App, you could manually set values rather than using the "Reference Base Maps Option". This will allow you to provide the Name:Value pairs from a curated list of reference base maps.
The name will be the display name like you see in the screenshot you provided, and the value can be obtained in the XML view of the Report Map tool. Look for the "<ReferenceMap>" tag in the XML after setting the desired reference map.
Ah, I see now. You are correct that this will not be controlled by the App unless you want to render the map as an image before it is output. The spatial output does not have a reference base map associated with it. and theoptions listed there are set by the Gallery.
This isn't my area of specialty, so maybe @Claje or @JulieM could point you in the right direction.