Technically, there's no issue with mixing the twin systems and the slip systems. e.g.
sS = slipSystem.basal(cs)
tS = slipSystem.twinC1(cs)
ss=[sS.symmetrise; tS.symmetrise]
sSLocal = o * ss;
sigma = stressTensor.uniaxial(vector3d.X);
SF = sSLocal.SchmidFactor(sigma);
However, if you look at what you did earlier, it's just that you were rotating the twin system on into specimen/grains directions
and combing those then with slipSystems in crystal coordinates, followed by then using these with a stress tensor rotated into crystal coordinates. You can use one or the other solution - either rotate the slip/twin system or rotate the stress tensor - but don't mix the two.
Have a look here and try to understand what is happening:
http://mtex-toolbox.github.io/files/doc/PlasticDeformation.html#20
Cheers,
Rüdiger