Yes exactly, the site shows photos all taken from within the app. I have done A/B tests against photos taken in Camera.app and the Photosynthesis composite does significantly beat the detail central area covered by the second lens in Photosynthesis.

Because of the limitations of capturing multiple lenses at once through isVirtualDeviceConstituentPhotoDeliveryEnabled, there is a second capture mode in the app for 'Quality' which takes a simultaneous capture then takes sequential shots from each lens which do benefit from Deep Fusion, then uses those for the stitch (as long as the Deep Fusion images outperform the simultaneous capture results). That's also what I do for our Night mode.