Hi @Anonymous,
usually for very accurate reconstruction, such as those in archaeology, people strongly advise to take pictures in RAW format and then converting them by using LR or similar. The reason why you do not want to use jpeg from the camera is that the camera itself could apply filters or distruptive corrections during the internal process of compression from the raw format to jpeg. Also, there could be a lot more to say on the actual amount of features used by the software in the process of reconstruction or alignment, and hence, if the difference of bit depth may really have an impact.
So i agree with the common practice, that is, shooting in raw format, storing the raw photos as reference and then exporting to jpeg (at the highest quality) and using jpeg for reconstruction.
There is so much to read out there, but after i read tons of discussions and papers, so far no body has ever drawn an exhaustive conclusion on this matter.
V.