I totally agree with you regarding not calling the offside on Alcacer. However, they have treated handballs like that for quite some time now. If it's close range such that there is no opportunity to move the hand, then it's not a handball, unless the hand is in an unnatural position. If you look at both cases with that in mind, most refs would not call it.
Also, this was not a shit game plan by Valverde. They were playing against a weaker team in the league, at home, and with a lot of cushion in points. So, this was the right game for him to test his new formations with Cutiniho in the team. This was the right game to test the formations. He got lucky at the end. He will not do a test like this with Valencia this week. That was actually very smart of him to do his test in a game like this. He could have put his regular team in, but he was trying to get more than a win from this game.