Are end of round scoring of VPs done simultaneously at 2d. Pass Initiative?

no. It happens one step earlier during "End of round effects" (step 3 from"Status Phase" - p. 4 of Skirmish Rule). Then we follow the normal conflict resolution (p. 9 Timing p. 11 Conflicts - Rules Reference Guide): mission rules, player with init, player withour init. As most end of rounds VPs come frome the mission rules they are gain simulatanously. That is me opinion, however IF u want to get REALLY deep into it you can check THIS topic