Balance is by far the most complex aspect of a MOBA. If you balance it based on the actual capability of champions and how the game should be played, it'd be extremely imbalanced when it comes to how the game is actually played, and that changes even more so from region to region and rank to rank.
Every game like this, even 1v1 fighting games, have tiers of characters:
- Technically complex, fragile, high risk high reward, oppressive when played nearly flawlessly, moderate reward when played decently
- Tanky, technically complex, oppressive when played flawlessly, smaller reward when played decently.
- Balanced all around, fairly predictable, can take a few hits without dying, fairly forgiving but has a few favorable matchups against top tiers.
- Easy to play, predictable patterns, decent when mastered but top players will nearly always be able to outplay.
(this isn't all of them, just typical examples)
When you mix in items and build paths, runes and masteries, champion synergy, etc., it's impossible to make every champion perfectly balanced, and that was never anyone's intention. Some champions require a lot of knowledge to play well, not just technical skill. Some require more team coordination, some require certain matchups, some are more well-rounded but don't have situations where they faceroll without a significant early lead.
They are looking at a lot of data from a lot of regions, looking at power spikes, win conditions, play patterns, synergies, playstyle trends, so on and so forth. You could have every champion have a 49%-51% win rate and still have a very imbalanced and unhealthy game.