It's not obvious that he needs to be in the cockpit, rather it's obvious that there is no security threat to allowing a pilot to occupy the jump seat. The trust they're given to fly the plane is a superset of the trust required to be in the cockpit at all.
I recommend watching the Blancolirio channel on YouTube, Juan is a 777 pilot and has I think hundreds of episodes on crashes and near crashes that have occurred. Third pilots have saved countless lives.
The insane thing about the Lion Air Flight 610 crash is in the same plane a day before it was avoided because the 3rd pilot who didn't have to follow any particular checklist realized there was a trim stabilizer issue and had the pilots turn it off.
Now, I have no idea why that plane flew again the next day at all. But it did with two pilots and all 189 aboard were killed.
In addition to training etc, yes there are positives to having a certificated third person for "crew resource management". They are expected to observe and speak up if the PIC and SIC miss something, and to help in an emergency. In UA232 for example, a third pilot was instrumental in saving lives; it took six hands to make the airport.
Makes life easier if one of the pilots needs to visit the loo or eat something, as long as the third pilot is type rated. And besides that, it can also be useful in the case of a serious incident to have a third capable person at hand to run checklists, communicate with engineering, navigation or whatever else.