> The confirmation vote is not just about the President of the Commission but the entire package, including other major positions in the Commission and major policy directions

It's two votes, not one; the President and the rest of the Commission are confirmed separately. In this case there was a four month gap between the two votes!

VDL was confirmed by the Parliament on 16 July 2019, by 383 votes to 327 against, with 22 abstentions[0].

Her Commission was approved by the Parliament on 27 November 2019 by 461 votes to 157 against, with 89 abstentions[1].

[0] https://www.europarl.europa.eu/news/en/press-room/20190711IP...

[1] https://www.europarl.europa.eu/news/en/press-room/20191121IP...