Swings and roundabouts, different compromises, is the answer.
As noted, 2 engined a/c by regulation end up with significantly more thrust when all engines are operating than a 4-engine aircraft, assuming both meet the mninima for one engine inop.
That makes two engined aircraft less close to the design goal for AEO ops, since they are 'overengined'. That's usually bad. (in terms of design optimization).
It also gives a typical two engine aircraft more performance margin for AEO - e.g. for windshear. that's good.
Four engined aircraft can afford to lose two engines. Two engined can't, obviously. Four engines good.
But four engines instead of two means roughly twice the inflight shutdown rate. So four engined aircraft have more engine failures. That's bad.
Four engined aircraft may well end up lighter (due to less thrust excess by design). That's good.
But 4 sets of engine 'stuff' - gearboxes and nacelles and the like - may weigh more than two sets of bigger stuff. That's bad.
And twice the number of engines may cost more to operate due to maintenance and the like.
In the end, someone waves their hands in the air and does a few sums and tries to guess which will be better. Sometimes it just comes down to what's available - if you're designing a new a/c and don't want a new, expensive, engine, you may have to choose it off the shelf. that may limit your choices such that only one of the two options is viable.