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Found the solution in the find_obj.py sample. The catch is that the C++ code is expecting a "two-channel or three-channel floating-point array, where each element is a 2D/3D vector", which translates in Python/NumPy to a 3-dimensional array.

import cv2
import numpy as np

a = np.array([[1, 2], [4, 5], [7, 8]], dtype='float32')
h = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype='float32')
a = np.array([a])

pointsOut = cv2.perspectiveTransform(a, h)