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I was in error earlier today when I said that the Twins had exceeded their signing bonus allocation. It seems I misinterpreted the article by Jim Callis linked to in my post. Instead of those totals representing the signing bonuses of players selected in the first ten rounds of the draft, they were the overall totals.
The article I had been looking for is this one, where we see that the Twins were under their bonus pool spend with a total of $11,938,900. This actually comes in $32,500 lower than my estimate when I posted this update about three weeks ago.
In total, Major League Baseball spent 97% of the bonus pool, and coming in below the full amount can be attributed fully to Mark Appel refusing to sign with the Pirates (who were willing to go over slot as far as they could go without surrendering a future draft pick).
The closest any team came to surrendering a future pick: the Blue Jays, who spent exactly 105% of their bonus pool.