I’m implementing a 12 pulse thyristor bridge for an HVDC rectifier station to validate a mathematical model, which takes the converter transformer just as a simple series leakage inductance Llk. How can I configure the Ydy in PLECS to implement that Llk?

You can set the secondary / tertiary winding inductance and resistances to zero. The saturable inductor model used to represent the magnetizing inductance is not as straightforward to disable, as there are certain restrictions on the saturable inductor’s parameters . I would recommend breaking the library link for the transformer (Right click + Subsystem + Break library link) and then simply removing the magnetizing inductance from the model.