IIRC, they have multiple quali sessions, with different drivers required to take part in each, and their times are averaged.

How does qualy work when there’s three drivers?

I don't usually watch the GT World stuff (my go to endurance racing series is WEC) but usually there is either a rule who has to do qualifying (in a mixed team of pros and an amateur driver the amateur has to do it) or teams can decide on their own.

I noticed late that NLS3 overlaps with GT World Challenge Europe, so I watched NLS instead and only looked up the result later.

Note that in sportscar racing there isn't that that much classification bonus and sponsorship money the teams just get, so they often rely on a paying amateur to fund the operation. That's the reason why in LMGT3 of WEC the bronze/amateur driver has to do qualifying and why there is a minimum driving time in the race for them. Notable examples are Ben Keating (owner of a series of American car dealerships) and Thomas Flohr (owner of Vista Jet airline).

I’m just waiting for f1 to pull a dtm and switch to gt3 cars

The loudest shouting "F1 2026 regs bad" people essentially want F1 to become IndyCar where all manufacturers leave and only Mercedes and Ferrari remain who then supply the rest.