Let's talk about the 'same car' thing.
The cars are from the same engineering firm.
They are setup by different teams of people, worked on by different teams of people, and maintained by different teams of people. There is overlap, of course, but the cars' basically have their own groups individually for specific tuning/troubleshooting/telemetrics.
If you think Valteri is getting the best and fastest crew to work on his car, the question turns into "Why would Mercedes use their best and brightest on their second in points?"
The point is : there isn't a handicapped car per se, but one of the two teams that gravitate around the drivers' is better at it's job -- thus, one of the cars has an edge.
It's a simple concept, but it has to be true. Mercedes can't simply clone their driver-centric teams over and stamp them to both sides -- so they have to prioritize their better driver having the faster team with more skill and better communication.
Sucks for Valteri, but as we've seen race after race -- he gets by just fine.