If the form of the ceiling is purely 2.5D, i.e. no occlusion from anything hanging whatsoever so you can see everything from above that you see from below, then you could just generate the orthomosaic as a top view rather than a bottom view, but for anything more interesting i don't think there is a solution within photoscan.
I think the only other thing to do is mirror it in external software, or attach it to an acad drawing and mirror it there (which is my preferred thing as the dwg file can also include any notes about what whether it is a reflected view or not and additional measurements, coordinate system etc)