I'm not sure what your picture is meant to represent. I'm not drawing 45 degree lines. (I would have eventually - I wanted to be able to rotate. But if it doesn't work properly in the axis-aligned cases, rotating is only going to make it worse.)
Let's say I have an arbitrary polygon and I want to draw a border around its edge. The natural choice would be a polyline, At least in all other graphics systems I've used, that would be the case, and the line width would be uniform. I'm not sure what the use is for a polyline function if, as soon as you deviate from a single straight line, the edges distort.
Here is an extended case, though not more complex.
func _draw():
var points = PoolVector2Array()
points.append(Vector2(0, 0))
points.append(Vector2(0, 100))
points.append(Vector2(100, 100))
points.append(Vector2(100, 200))
points.append(Vector2(200, 200))
points.append(Vector2(200, 300))
points.append(Vector2(300, 300))
points.append(Vector2(300, 400))
draw_polyline(points, Color(1, 1, 0), 16)
The result is this:

The line is just fine everywhere along its length - even at the inner joins - but not at the ends. If it can draw it fine everywhere else, why not the ends? Alternately, If I do want a true polyline without distorted ends, how do I do it?
I tried out draw_multiline. I had to double up the internal points:
var points = PoolVector2Array()
points.append(Vector2(0, 0))
points.append(Vector2(0, 100))
points.append(Vector2(0, 100))
points.append(Vector2(100, 100))
points.append(Vector2(100, 100))
points.append(Vector2(100, 200))
points.append(Vector2(100, 200))
points.append(Vector2(200, 200))
points.append(Vector2(200, 200))
points.append(Vector2(200, 300))
points.append(Vector2(200, 300))
points.append(Vector2(300, 300))
points.append(Vector2(300, 300))
points.append(Vector2(300, 400))
draw_multiline(points, Color(1, 1, 0), 256)
And here is the result:

This doesn't have the distortion - but then it doesn't have the width I gave it either. (I bumped it up to 256 to see if that made a difference, and always had single pixel width - it ignores the width specified.) So that seems to have its own bug.