Ok I found a little trick. It's not exactly what I wanted but it's ok for what I needed.
I take the common parent of both parents (manually here, but I'm sure there're ways to find it programmatically).
Then I can take the relative transform from both nodes to the parent and calculate the delta vector
var t1 = bone1.get_relative_transform_to_parent(common_parent)
var t2 = bone2.get_relative_transform_to_parent(common_parent)
var p1 = t1.xform(Vector2(0, 0))
var p2 = t2.xform(Vector2(0, 0))
var d = p1 - p2
Just in case anyone else needs this.