I think perhaps (and I could be wrong) your understanding of the Win% numbers from FanGraphs is not quite right. That data is very interesting, but I am guessing it doesn't mean what you think it means. I don't have much time to explain it all right now, but I will take a short stab at it. Here is the definition from FanGraphs: Win Expectancy is “The percent chance a particular team will win the game based on the score, inning, outs, runners on base, and the run environment. These percentages are calculated using historical results of thousands of real MLB games, meaning if a team is losing and has a 24% win expectancy, only 24% of teams in similar situations in the past have ever come back to win."
Notice that the definition does not say anything about the value of a run, because you don't know the actual value of the run until the game is over. You mentioned earlier that the Win%'s can change faster in the late innings and this is true
if the game is close, but it is not true if the game is lopsided. An early run doesn't swing the percentages as much as a late run in a close game, but this is only because at the time you don't know how many runs will be scored later. Historically, any given situation was followed by a wide range of possible outcomes. Sometimes that run was the last run scored in the game. Sometimes there were many more runs scored in the game. Because there is such a wide range of possible outcomes you can't say with any certainty how much that run is worth until the game is over.
In a 1 run victory, every run is worth the exact same amount because you needed every single one of them in order to win the game. In a lopsided game technically all the runs are still worth the same as each other, but essentially the early runs were the most valuable because they were the only runs you needed to win the game.
If this doesn't make sense to you I guess we will just have to agree to disagree on this issue, which is fine.