Watch 1B Years of Tectonic Plate Shifting in 40 seconds (youtube.com)

I also had the same thought, also the projection leads to strange stretching and I can’t tell what’s geologic and what’s distortion.

As a geologist I'm intrigued by the possibility of adding such 'fog of war' but I believe that, if possible, it will make these palaeogeographic reconstructions a little pointless. First of all you have to define what you mean by "have no idea about". Even if there aren't any outcropping rocks of a given area representing a given geologic time span, it doesn't mean that we cannot know anything about their previous existence. We can collect palaeographic information from many proxies, e.g.: single crystals in sandstone, presence of ophiolites, plate motion speeds, residual soils characteristics, fossils, accretionary arcs' structure, ocean water palaeo-geochemistry, sea level changes, teleseismic data, metamorphic rocks among many others. Even a lack of information is an information sometimes. In some cases we can have more info about a subducted area than of a "ever existing" inner craton. Geological record is discontinuous by nature, everywhere. If a strict "only rocks outcropping in the same form they were emplaced" rule would be enforced, only a few pixels will be visible. A map of the uncertainties will be really interesting, I agree, but it will be multidimensional and not easy to read on 2D.