From experience of travelling with a non-EU resident (my wife), she will either have to present herself at a check in or transfer desk, very occasionally she has a visa check at the gate.
For EU flights as an EU resident (as is the OP) your ID is checked at the gate or at a passport booth when going from Schengen to non-Schengen, but the checks are less stringent (and I would guess that the boarding checks are less stringent than the booth checks).
So checks are essentially different depending on circumstance. You'd find the same if you were travelling to the US or China for example.