That's a great explanation of why popular champs can't be overpowered and I agree with it. It doesn't explain why they should LOSE winrate i.e. go below 50 just because they're popular.
Imagine riot released a champion tomorrow that was just the most fun champ they ever created, it's actually really balanced but it's so fun that everyone wants to play it and it gets a really high pickrate. I don't think that champion should be made weak just cos everyone loves playing it?
To be fair, winrate has to come from somewhere. Not every champion can be >50%. If unpopular/niche champions are >50, and popular champions are 50, who's below 50%? In addition, the total pick-rate of all <50% champions needs to equal the >50% champions. As such, super popular picks being <50% affords the most other champions to be strong/viable.