I tried shift+right-click and it worked, but only on certain tiles. Maybe it's a bug? I think it has to do with the tiles rotation... I'll try to report it but thanks for the heads up!
And yeah, it really sucks having to use 3rd party tools for that. I tried using Tiled a few times but I think it's unnecessarily complicated. C2 tilemap object is pretty easy to use but I lose so much time having to pick the tiles manually from the bar.
I'm actually using another tool now called Pyxel Edit which is pretty good but it only exports to .json/.txt/.xml and so I can't import the tilemap into C2, and still I would have to manually change a few things later so it wouldn't matter anyway..