Shapes
Each region of the softbody has one collision shape, on its rigidbody. To see them, turn on Shapes in Debug Draw, which works in the editor and in game:

The actual hierarchy inside the node is as follows:
- RigidBody2D: contains
- CollisionShape2D
- RemoteTransform2D (moves the bone that deforms the texture)
- Joint2D nodes, one per neighbour
Shape properties
The Shape parameters section contains:
- Radius: the size of the shape. Circles get half of it as their radius, squares get it as their side. It defaults to a little under Vertex Interval, so neighbouring shapes nearly touch.
- Shape Type: Circle (the default) or Rectangle.
- Edge Clearance (in the Region section) keeps every shape just inside the texture, like this:

Circles or squares?
Use circles on the hexagon pattern. A square the size of the spacing already overlaps its diagonal neighbours at rest, and once rotated its diagonal reaches its second neighbours, which do collide: 40 to 86 self contacts on a resting softbody against 2 with circles. Squares still suit the rectangle pattern. The editor warns about squares on hexagons.