I already got part of the answer in thread. Which says that if I want to perform a state tomography on a known state, the estimation can be simplified.
In the case of "GHZ-class", citing from the thread above: if the state is $|\psi_{a,b}\rangle= a|000\rangle+b|111\rangle$, then $$\langle XXX\rangle = 2ab, \qquad \langle YYY\rangle = 0, \qquad \langle ZZZ\rangle = a^2-b^2,$$
Now the point is that I am actually trying to optimise QPT for logical computing, for the case of operation between two logical qubits, both encoded in GHZ-class states.
The computation is also logical, so I wonder whether the above equations still hold after the gates.