Hm... making JohtoMap compatible with Pokémon Crystal wouldn't be a bad idea, actually. :)
But if it seems this map editor won't be updated anymore, then I guess it won't be added. However, 1st and 2nd generation seem to have the exact mapping engine, except the 2nd generation has the palette changes for the real time clock. But the 1st generation does indeed use different palettes for every map, so it would show up in those palettes on Super GameBoy or Pokémon Stadium.
If there was a map editor for the 1st generation that would load all the tiles from the ROM itself, then it would be great.
However, I do see that hex editing the 1st and 2nd generation is much quicker than any other generations.