Then player A gets BiS legendaries, while Player B gets the !@#$ tier legendaries that are totally useless. Fast forward some time, Player A and Player B both try to get the same spot in a raid. Of course, player A gets picked because he has better legendaries that actually increase his performance.
Well in this scenario as Player B has been helping their guild out more than Player A has, I think most communal focused guilds would prefer to give the spot to someone like Player B who is actually contributing to helping the guild, rather than the person who got lucky and is simply there for the ride.
Also as Player B has spent more time doing current content than Player A, they will arguably know how to adapt and adjust to situations (like where they can squeeze out more DPS for example) more readily than Player A will.
There are plenty of groups and guilds clearing Normal and Heroic Emerald Nightmare & Trial of Valor with most of their roster not even having a BiS Legendary. A Legendary should not going to be the sole determining factor in whether or not a coordinated group is going to beat an encounter. Sure, the Legendary might bring enhancements or utility that may make the process smoother, but they're not a through-and-through substitute for skill and execution.