Tool/software:
Unfortunately TI decided to lock my ongoing issue (https://e2e.ti.com/support/power-management-group/power-management/f/power-management-forum/1490233/tps65279-strange-behaviour-on-pgood-pins/). To help others I will write the solution here.
Ti told me via mail:
Until the EN pins or VIN aren’t high and present, there is no valid usage of the PG pin and it’s outputs.
Case 1 – VIN is high/Low, EN is Low – PGOOD is invalid
Case 2 – VIN is low, EN is high – PGOOD is valid and would be low
Case 3 – VIN is high, EN is high – PGOOD will go high after FB voltage goes above 94% of the target value.