Discovered that Geometry2D.is_polygon_clockwise is actually backwards.
func clip_outlines(outlines: Array):
# First, filter out the holes
#
# Note that holes are counter-clockwise, but Godot's function
# to detect clockwise polygons is backwards.
# See godotengine/godot#49716
var holes = []
for i in range(outlines.size() - 1, -1, -1):
if Geometry2D.is_polygon_clockwise(outlines[i]):
holes.push_back(outlines[i])
outlines.remove_at(i)