The blackout window will change for those two nights. It looks like it will start around 4:30pm/5pm and then open back up at 10pm eastern. Now those games on during the day may or may not get on MLB Extraing Innings. I have no doubt mlb.tv will carry them. Teams are not being allowed to televise in that window, but are in what would normally be the blackout window instead.
They did and actually its an exclusive window and not just a blackout window. No TV by any team during that window. This is why most teams are going to play durinig the early afternoon to avoid this exclusive window. Remember even ESPN alternated their contract with MLB during their contract. Secondly, I suspect the wording in their contract didn't specify a time this time, but an amount of time in and around their game. They have considering doing a night game for more than a year now. I suspect that this was wrote into this contract they have now and left them an option to do something like this. Which is why they are avoiding the slot like the pague. It is no different than the Exclusive rights that Versus has, which results in NHL teams avoiding that night and slot in the US. Those teams that play during it lose the ability to put a game on tv.