Ah, I think I've found the/a solution. At least, for a BoxShape collider, this behaved as expected (i.e., by increasing SPEED, it causes the RigidBody to collide more quickly, and with more "empty space" where the MeshInstance doesn't cover it, with a StaticBody positioned beneath it):
var SPEED = 1.0
func _ready():
self.shape.extents += 2.0 * Vector3(SPEED, SPEED, SPEED)
print("extents: ", self, self.shape.extents)
EDIT: And something similar works for a more general ConvexPolygon shape collider, lovely:
func _ready():
print("points: ", self.shape.points)
for i in len(self.shape.points):
self.shape.points[i] = 4.0 * self.shape.points[i]