Hello devliam :),
Parts like road, water and mountains are stored in 3x3 tiles + an additionnal 2x2 (above) to cover every possible angle. It's all manual for now.
In the subfolder rpgmaker/ I've added an autotile tileset file for roads, but it's arranged for this software only.
I plan to arrange the atlas for other softwares (such as unity, godot, gamemaker, gbstudio, ...) in the future.
Do you have any suggestion about that ?