It is my understanding the B&W microfilmed Sanborn maps were produced from the LoC’s color originals.
So the color ones available on-line from the LoC scanning project *should* match the microfilm versions, just in color.
The “overlays” seem to mostly occur starting in the 1930s (from Bureau of Census Sanborn books that were given to the LoC?)
Although I am sure overlays were used earlier, the maps were “completely” redraw relatively frequently [depending on the city/town] before then, so the need was less. (or maybe just the LoC collection only had the original books, and did not subscribe to, or paste in, the updates, whereas the Bureau of Census did?)
If you are interested in which sheets have B&M trackage, see:
(although checking now, it looks like I need to re-do all the links…)