What car(s) are you referring to? Can you post an example/examples? As far as I know, most all E500Es only had the paint code used in the "Paint 1" data field, as seen on my (attached) data card for my car.
Paint 2 would indicate a second body color, as a two-tone paint car. This was seen often in 1950s and 1960s MB models, such as the Pontons, Finnies, 114/115, and 108/109 models, where the lower body color was one color, and there was a second color for the A and C pillars, and roof.
It certainly could -- and did -- also indicate the color of the hard-top on R113 and R107 roadster models, if so ordered with a different hard-top color. This was actually quite common back in the day for the roadster models, but I think went out of fashion during the 1970s. I'm sure it could have applied to the R129, as well, though I don't know that many US-spec R129s were actually ordered with different-color hardtops.
In recent years, a lot of Maybach cars have shipped with two-tone paint from the factory.