Yes the order matters since within a given noise level, there are many models that can explain the data. Settings related to search method, search options and initialization method all matter. In this example, an initial model is first generated using instrument variables. This model is different when the inputs are swapped. You can enforce a closer agreement by using a different initializer, but there is not gaurantee, or a way of enforcing, a strict match. The following seems to work better here:
steam2.InputName = {'MagVolt1';'Pressure1'};
steam2.OutputName = {'GenVolt1'};
m1=ssest(steam1,2);
m2=ssest(steam2,2);
sys1 = tfest(steam1,m1);
sys2 = tfest(steam2,m2);
figure
bode(sys1,sys2(1,[2 1]))
figure
compare(steam1,sys1,sys2)
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