I agree that $Y$ is not the best notation. Actually, in the paper that I was referring in the answer there was a gate $Y$ that was doing the desired job (it was also not a self-inverse gate). I didn't use the gate from the paper, but I kept the notation. Anyway, I like more Craig Gidney's suggestion to use $H_{YZ}$ gate. I will edit my answer to replace Y gate with $H_{YZ}$ (but I will call it just $H_y$ in order to have a short name in the circuits).
Now, about the question. I tried to do implementation of the circuits with Qiskit and find out that their outputs are the same. But, firstly, note that, my definition of $Y$ gate is different from the definition mentioned in the question. Here are my notations and corresponding Qiskit implementations of those gates:
\begin{align*}
Y = \frac{1}{\sqrt{2}}\begin{pmatrix}
1 & -i \\
1 & i
\end{pmatrix} = &u2(0, \pi/2)
\qquad
Y^{\dagger} = \frac{1}{\sqrt{2}}\begin{pmatrix}
1 & 1 \\
i & -i
\end{pmatrix} = u2(\pi/2, \pi) \\
&u2 = \frac{1}{\sqrt{2}}\begin{pmatrix}
1 & e^{i\varphi} \\
e^{i\lambda} & e^{i(\varphi + \lambda)}
\end{pmatrix}
\end{align*}
Here is the code:
from qiskit import *
import numpy as np
simulator = Aer.get_backend('statevector_simulator')
q = QuantumRegister(2, 'q')
circuit_xz = QuantumCircuit(q)
circuit_xz.h(q[0])
circuit_xz.cx(q[1], q[0])
circuit_xz.rz(np.pi / 3, q[0])
circuit_xz.cx(q[1], q[0])
circuit_xz.h(q[0])
circuit_yy = QuantumCircuit(q)
circuit_yy.u2(np.pi/2, np.pi, q[0])
circuit_yy.u2(np.pi/2, np.pi, q[1])
circuit_yy.cx(q[1], q[0])
circuit_yy.rz(np.pi / 3, q[0])
circuit_yy.cx(q[1], q[0])
circuit_yy.u2(0, np.pi/2, q[0])
circuit_yy.u2(0, np.pi/2, q[1])
circuit_xz_yy = circuit_xz + circuit_yy
circuit_yy_xz = circuit_yy + circuit_xz
result_1 = execute(circuit_xz_yy, simulator).result().get_statevector(circuit_xz_yy)
result_2 = execute(circuit_xz_yy, simulator).result().get_statevector(circuit_xz_yy)
print("The first result \n{}".format(result_1))
print("\n The second result \n{}".format(result_1))
And here is the output:
The first result
[ 0.375+0.64951905j 0.375-0.21650635j -0.125-0.21650635j 0.375-0.21650635j]
The second result
[ 0.375+0.64951905j 0.375-0.21650635j -0.125-0.21650635j 0.375-0.21650635j]