I'm with WheresMyElephant on this. The lists help evaluate cards at a given price point because you will often be choosing between cards of a given price point depending on how much money you have on your turn. Certainly cards are better or worse depending on the board, and you will of course sometimes buy a cheaper card than you could have, but it's pretty rare (though not unheard of) to buy an Herbalist for $11.
An argument for putting overpay cards on higher cost lists is that you can end up paying MORE for them. Border Village always costs $6, no matter what you gain with it. And even if you end up having more than $6 available, you always get the same benefit out of BV. Peddler never costs more than $8, so it still makes sense to compare it to the other $6+ cards. If you have $6+, chances are you can pay for Peddler. No matter what you pay for Peddler, the benefit will be the same. I admit, Peddler is more of a stretch here because you usually end up paying $0 or $2 for it, but at least you can afford to buy Peddler when you are considering the other cards on the list.
The overpay cards are different because you will often be paying MORE than the listed cost and the benefit scales up as you pay more. When you overpay $3 for Doctor, you have effectively purchased a $6 card with an on-buy bonus of trashing cards from the top of your deck. Yes yes, edge cases with TfB, Haggler, what have you. But Doctor-at-$6 is not meaningfully comparable with Woodcutter. It compares with other $6s. When I have $2 available, I am choosing between Squire and Stonemason, not Squire and Stonemason-that-also-gets-me-two-GMs.
Another issue is that if you don't separate the overpay effects in some manner, people are going to evaluate these cards in wildly different ways. This very discussion is proof of it. There is already some difficulty with the lists as they are -- some people value potential impact while others prefer consistency. Should I rank a card higher because it is always a useful addition, or should the top spots be reserved for potential high impact game changers, even if they are terrible 90% of the time? But whatever, that's fine. With the overpay cards, OTOH, some people may put little emphasis on the overpay (man Stonemason is bad at $2) while others will focus on it entirely (heck yes double Possession with $8p, what an awesome $2 card).
I guess what I'm trying to say is, this is all very confusing and let's argue some more.