But that's where I'd think that no, the benefit of the while-in-play effect is not received even though it was set up twice, especially since it's different wording from other existing cards with the same effect such as Bridge. I'd intetpret that as performing the check twice, but you can't get the benefit more than once per physical card.
For me, while-in-play means the same thing whether or not it is below a horizontal line, considering the context of Dominion as we know it.
Why is while-in-play special? Everything else means different things depending on whether or not it is below a horizontal line, so it would make a lot of sense for while-in-play to follow the same logic as well.
The wording is different from other existing cards such as Bridge because "When you play this, while this is in play, cards cost $1 less, but not less than $0" is
very much different from "When you play this, cards cost $1 less, but not less than $0 this turn". The former results in games like
T1: buy Highway Without Horizontal Line.
T2: buy nothing.
T3: play Highway Without Horizontal Line, cards cost $1 less while it's in play, but not less than $0 now, buy a Silver.
T4: buy a Silver.
T5: play the same Highway Without Horizontal Line, now there are two "while this is in play, cards cost $1 less, but not less than $0" effects, and since it happens to be in play now, all cards cost $2 less. Buy another Highway Without Horizontal Line.
T6: Your opponents play a bunch of Governors and Council Rooms until you reshuffle and draw one Highway Without Horizontal Line. Then you play it. Now you have to know if it's the one you bought on turn 1 or the one you bought on turn 5, because if it's the one you bought on turn 1, cards cost $3 less now, but if it's the new one, they just cost $1 less.
because "While this is in play" effects are continuous, so you get another one of those continuous effects every time you play it because that's its on-play effect, and then they build up. The latter doesn't, because even though "this turn" effects are continuous as well, they end after "this turn" is done, and there will never be another this turn ever again.
It's not that a check is being performed twice with Throned Highway Without Horizontal Lines, it's that a check is being performed continuously, for two different instances of the effect. The card is in play, so the check returns true for both instances.
The context of Dominion as we know it already has Scheme and Herbalist having the same wording without a horizontal line and below a horizontal line, respectively, doing different things because of that. I don't see a reason to believe that while-in-play is somehow special.