We are working very hard on the tileset right now. Hexagonal tiles are a pain to use because there are many more border configurations than with square tiles (of course, if you don't mind the borders, it is not a problem).
So it means making a lot of variation for each tile (even if we were to force convex area of a given terrain), and then finding the correct tile for each terrain type depending on its neighbours. It would obviously not be very efficient to do that all by hand(that is what we had to do for the first test map).
For instance, we had to manually pick the relevant wall section or swamp section (there are 64 configurations for swamp/grass, and 50 for walls), which was a very slow and boring process.
But Tiled is pretty awesome, and has a powerful automap function.
We specify "rules" (ie condition on tiles in a layer), and it generates output tiles when we press A.
Exemple of rule :
There are 4 layers combined for this rule :
The region layer tells which areas to consider for matches (so it will try all hexes + neighbours looking for the pattern specified by input and inputnot).
There are 3 regions of 7 hexes there.
the input_groundtype layer has some tiles with a swamp terrain type (in red there) + the middle one (but it is covered by the output tile).
the inputnot_groundtype layer is the reverse of the input_ground layer (it is not visible there, but the tiles with region have a red swamp tile in the inputnot_ground layer).
And finally, the output_ground, which specifies the tile to use when the condition is matched.
So all there is to do, once the rules are specified is to fill the map with generic terrain type tiles and height levels, as follow, and it is transformed into the map you saw above.
In conclusion, I cannot recommend
Tiled strongly enough. Sure, there are things that will be better done by a custom solution, but for the terrain edition itself, it is pretty awesome, and it has an unity plugin.
I wish I had known it to do my custom PnP RPG maps back in the days