Flux and torque estimation for driving PMSM with DTC

Torque can be expressed, in any orthogonal reference frame, for every motor, as the vector cross product of flux and stator current.
If you consider the total stator flux, this is nothing but the integral V-R*I, since the inductive and back-EMF voltage components can be all written as the time derivative of flux.
Maybe, the output of the model in Simulink is the rotor flux, which has the self-inductive flux (L*I) subtracted: flux_rotor = integral(V-R*I) - L*I ...

For simulink PMSM model, you'll have to determine if your motor is salient or non-salient one.. and other important parameters. Once you understand the Space-Vector theory you wouldn't even need the variable frequency drive (just generate the voltage vectors yourself), at least for first evaluation. however, if you do want to use the simpower blocks for the VFD, that'll be tricky (to connect the realized equations in simulink to simpower blocks).

Regarding the offset - it is known in real applications that in low velocities the flux integral drifts (because not all voltage phenomena is taken under consideration when writing int(V-IR))