In case any of the following paragraphs are confusing, just remember: Scott Boras is Pedro Alvarez's and Eric Hosmer's agent, and his side of the grievance is being argued by the union. The Pirates' side is being argued by the commissioner's office or Major League Baseball.
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It looks like the union will argue that there was a phone call from Scott Boras to the Pirates at 12:02 AM, and that was the phone call in which Alvarez agreed to sign with the Bucs. Unless Boras recorded all his calls that evening (and I wouldn't put it past him), this looks like a he-said-she-said type of situation, since it appears there were also calls between the two parties that took place before midnight. It looks like the Pirates will claim that Alvarez's "I accept" claim came at 11:58, and it appears to me that it will be difficult for Boras to prove otherwise. (I'm not sure who has the burden of proof in this situation, but my guess is that it would have to be the union, which is the party making the allegation.)
Barring some new piece of evidence emerging, it looks like the union's strongest case will involve making the case that the signing had not been formalized with the commissioner's office until after the deadline. Even the Pirates concede this, Kovacevic reports.
This is where Royals prospect Eric Hosmer comes in. Hosmer is also a Boras client, and there's no indication that he or Boras are unhappy with his bonus, which (it appears) also was not official until after the deadline. If the union makes the case that the Alvarez signing was not official until after the deadline passed, they would seem to be screwing up the Hosmer signing too, and nobody wants that.
Kovacevic also reports that Hosmer's removal from game action has been requested by Major League Baseball. So the commissioner's office is effectively holding Hosmer hostage until after the grievance is resolved. They're telling Boras that if Alvarez goes down, they're going to try to take Hosmer down with him. Based on all the evidence I've seen, they will probably be successful, if it comes to that point. It seems to me that you can't get rid of one signing and keep another that happened under similar circumstances just because the agent behind both wants to change one and not the other. It's both, or neither.
Because of this, it seems very likely to me that Hosmer ends up staying with the Royals, and Alvarez with the Pirates. It's possible that the arbitrator will agree that the commissioner's office should stop granting deadline extensions, but that the ruling will apply to future cases. Beyond that, I can't believe Boras will sacrifice Hosmer's massive bonus and potentially seriously damage his career. If Boras did that, I can't imagine why another amateur would want to work with him. So I don't think it's likely that this action does anything positive for the careers of Alvarez or Hosmer. This seems to be all about Boras flexing his muscles.