UCC28910 transformer dot convention

The auxiliary has the same phase as the secondary, so it is a scaled version of the secondary voltage. This allows the bias winding to be well regulated as the input line voltage varies. (If the auxiliary winding was in phase with the primary, the bias voltage would vary with Vin).

I that case pin 5 of the transformer is positive then pin 4 will also be positive according to dot convention..
the positive input goes to ground and what about the VDD pin

The bias power is supplied during the flyback interval, when pins 2, pin 8 and pin 1 are positive, not during the primary on time when pins 4, 5 and 7 are positive.

During the primary on time, D4 is reverse biased, during the off time (or flyback interval) D4 is forward biased and the Vdd cap is supplied.