I expect they'll get it done. As CD notes, it's typical Scott Boras to drag things out - even to the point of reneging on a draft day agreement, if they can get away with it.
But I think Stott will sign. A couple of reasons: First, Stott has a reputation as a high-character guy, in addition to being an outstanding prospect. If he reneges on a draft-day deal, and refuses to sign, that's out the window. His character is suddenly, and permanently, judged as equivalent to J.D. Drew: maybe a devout evangelical, but one who operates from the "I'm saved, so I can do whatever I want and still get to Heaven" modality.
Second, unless Stott is prepared to spend some time in independent ball, to the point that no team holds draft rights, he'll never see another bonus offer equivalent to what the Phils have on the table. College seniors simply don't get multi-million dollar bonuses, because they have no realistic alternatives to signing for whatever the drafting team will offer. So unless he's prepared to go independent (or to Japan or some such), this month is is best payday opportunity. Boras knows this.