I don't believe there's any systemic differences between the two cars we don't know about (i.e. upgrades go first to Max and Yuki running the old floor because he broke the new one, etc), I think it's more down to team focus, car development, and talent. Red Bull is completely focused on Max, and only runs the second car because it has to, and that has to make things hard for the second driver mentally as well as meaning that the car hardly ever develops in the direction they prefer and they don't even get as much help with setup, etc. and are guaranteed the inferior strategy. We've seen with Albon and Checo how a driver can start out doing okay against Max but fall further behind as time goes on, as the mental pressure of being unable to match Max takes its toll and magnifies in a completely unsupportive environment. Meanwhile, Newey builds cars that go as fast as possible and sees the drivers job as to shut up and drive it rather than compromising for their benefit, which has produced an extremely hard car to drive and amplifies every difficulty the second driver has.
I do wonder how different Albon's time in RB would have been without those two incidents with Lewis. A solid podium in his first season at Brazil would have put him just 3 pts behind Max in the tally of points in their races together, and a win in 2020 could easily have given him the confidence he needed and a base to build from. We will never know. He's certainly the post-DR driver who has come closest, but also one of many who were underprepared: Gasly was in his second season, Albon hadn't even had that much time, Lawson likewise, and whilst Yuki is certainly experienced giving him the car mid-season robbed him of time to prepare for their seat and learn the RB before he hit the track.