Based on David Zwicker's input, I was able to get transparency working by setting the facecolor directly as a 4-tuple with alpha.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import mpl_toolkits.mplot3d as mp3d
bot = [(0, 0, 0),
(1, 0, 0),
(1, 1, 0),
(0, 1, 0),
]
top = [(0, 0, 1),
(1, 0, 1),
(1, 1, 1),
(0, 1, 1),
]
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
face1 = mp3d.art3d.Poly3DCollection([bot], alpha=0.5, linewidth=1)
face2 = mp3d.art3d.Poly3DCollection([top], alpha=0.5, linewidth=1)
# This is the key step to get transparency working
alpha = 0.5
face1.set_facecolor((0, 0, 1, alpha))
face2.set_facecolor((0, 0, 1, alpha))
ax.add_collection3d(face1)
ax.add_collection3d(face2)
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