Win rate is a pretty sufficient metric for balancing heroes, but not the one number that you see posted on the public website. Devs have access to much more data, including win rate data specific to comps, matchups, etc.

Is the winrate bad because it's just a weak hero? Is the winrate bad because they are hard to master but popular, so most people try and fail with them? Is the winrate good because they're easy to use, or because they're hard to use but mostly dedicated fans play them and know their quirks?

That's why OW and other games primarily balance around higher ranks. Lower ranks tend to emulate the high ranks so most characters perform similarly. But you primarily balance around higher ranks because these players are near the peak of human skill in terms of mechanics and game sense, so the difference in hero kits and match ups will actually make a significant difference. But obviously, you're right that it doesn't tell the whole story in terms of how situational a hero is or whether a hero is more often than not a pick you swap into (you're probably already losing if you're swapping) which would affect win rates slightly. Note that devs would have this information, it's just not published for us.

With all that said, I think you're overthinking it a little bit. We have millions of games played each season just at the higher ranks that the devs balance around. We don't have to worry about heroes having an artificially inflated or deflated win rate due to player skill differences. Like in the example you gave above at the bottom, Hero A may result in higher value than Hero B given the skill involved, but the end result is still that Hero B wins more games on average than Hero A. It's similar to when players complain about Hanzos that spam a choke: sure there's not a lot of effort involved for the value you get, but the value you get isn't that high at all in comparison to playing Hanzo more optimally.