No doubt, but there's massive factors of difference in the game then and the game now. It's not unheard of to be an outlier like Ruth when the entirety if the league is basically a small sample size of players.
The talent pool wasn't even a pool, it was a talent puddle.
Yes Ruth was better relative to his peers, but when you have like 5% of the peers of today's baseball players, it's far more likely that there will be a statistical outlier. You're a science guy, so you should be familiar with the small sample fallacy.
So, while you are correct that it's unfair to compare Trout's skills vs Ruths, it's also equally unfair to compare the eras in which they played. Trout putting up the numbers he is putting up now is absolutely more impressive than what Ruth did back then