Hello there. The addition of analysis points does not change the system dynamics, but it does change the underlying LFT model. This introduces slight numerical discrepancies that accumulate to create a visible difference here.
systune has computation options that you can play with to minimize that difference. First, notice that when you run systune, both runs terminate at 500 iterations. That means they are reaching the default maximum iteration limit before they converge. Try extending that limit with the MaxIter option to get a smaller gap between the two answers. Second, systune starts its optimization from random parameter values, which means it can fall into different optimization minima depending on where it starts. The RandomStart option causes systune to try multiple different starting points and return the best optimization it finds.
opts = systuneOptions('MaxIter',2000,'RandomStart',5);
CL1 = systune(Gw1, Rtrack, opts);
CL2 = systune(Gw2, Rtrack, opts);
There is still a small difference between the two resulting systems, but it's below -60dB, which is the requested accuracy on the final value. You can reduce that even further using the SoftTol option.
opts.SoftTol = 1e-6;
CL1 = systune(Gw1, Rtrack, opts);
CL2 = systune(Gw2, Rtrack, opts);
% examine the difference between the resulting tuned systems
sigma(ss(CL1) - ss(CL2))
