Perhaps calculate mininum from r and r2, and then fill in between 0 and this minimum:
import numpy as np
import matplotlib.pyplot as plt
theta = np.arange(0, 2, 1./180)*np.pi
r = abs(4*np.sin(2*theta))
r2 = 2 + 0*theta
r3 = np.minimum(r, r2)
plt.polar(theta, r, lw=3)
plt.polar(theta, r2, lw=3)
plt.fill_between(theta, 0, r3, alpha=0.2)
plt.show()

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