I've placed them one by one, or stamp a couple of them (the cluster ones) sometimes with tiled - it wasn't too much work, but I had to create only one map.
These days, I'd probably use ldtk which is amazing. Especially if you need to produce multiple levels
I took a look at what Godot offers here by default and yeah, it seams too simplistic (or I'm missing something, which is probable) to achieve the effects as in the preview image.