The SYNC function of any LTC device is not modelled in LTspice (especially dc/dc converters). If an LTspice model has a SYNC pin, then it is normally because that SYNC pin is shared with another function and LTspice is modelling that second function and not the SYNC function. Hope that makes sense.
The additional pullup to Vcc is probably because of the leakage current of the VN2222. This can be as high as 200uA, so with just a pull up to VREF, would cause an excessive voltage drop across the pull up resistor. If you lower the pull up resistor value, it would cause too much stress for the output capability of VREF when the FET is ON. The extra pull up path to Vcc overcomes this. The diode stops Vcc back feeding into VREF.