Im having a hard time following what is making the US presidental system different from the EU commission?

the US president is appointed by politicians who are elected, and the only accountability mechanism for president is impeachment, which is again, indirect via elected politicians.

The EU Commission does the bidding of the elected EU Council. The Commission is sort of a civil service.

100%. This is why many of us have a problem with the EU. And world governments in general — the more power they have and the further away from the elections that keep them accountable, the more tyrannical they become.