The appointment of the commission president is quite different from how the German chancellor is determined:

1. The majority of representatives in Bundestag represents (up to rounding issues) the majority of voters.

2. Parties advertise their chancellor candidate before the election, and voters take that into account when choosing which party to vote for.

Being chosen democratically isn't a black and white thing. It becomes gradually less democratic as you separate voter intent and outcome further. This isn't just a function of how the election process itself works, but also voters being informed.

Practically no voter would have predicted von der Leyen becoming commission president when they cast their vote, making her appointment not very democratic.