Well, we'd have to see what the Phillies' record was at that point. Of course it would, but the competition might be more fierce then.
One of the players in that Passan article floated this very possibility a few months ago, of sitting out not because of the compensation change but because once teams are in the heat of the season their needs change and they become more desperate.
As for that WAR projection in the Zolecki article, for sure, if you think you have .5 starter in hand and Lynn only gives you 1.5, and you figure you can upgrade at the trade deadline, you're not gonna pay too much for a mere .5 WAR in the first half of the season.
I agree the compensation shouldn't faze the Phillies too much. They can trade for allocation, and can also acquire some lower-level depth from the 2018 draft class down the line, even if they are buyers (you throw in an extra AAA-level piece in exchange for an A-ball piece. Plus if they trade Hernandez it might not be for a major leaguer. Ditto Rupp or some of the starting pitcher spare parts).
On the other hand, giving up picks when they pick this high, and hopefully for the last time, when they are also almost certainly going to give up picks next year too, is a little questionable. But that's a call they already made with Santana.