The more I look at photos of the 1/4 JH, the more I think they did use stencils/decals as they did with the others, because the problems (with the brown dots at least) are consistent across all pieces. They're all pretty jagged, but the overlapping starts to happen in the same place on every statue we've seen.
If that's the case, these problems could easily have been avoided by just making a new stencil. Maybe they did it on purpose to set this "comic" version apart from the actual film version? But if that was their intent, why did they bother changing the two inaccurate pouches on his belt to the single accurate pouch?