HS pitchers have been taken first overall before, just never a RH prep arm. Groome had some questions off the field last year that led to his slip in stock. Moniak barreled up everything he saw during the summer at every high profile event. Has tremendous barrel control and great hands.
Goosegg hits it on the head. If you can sign any one of your top 3-5 with the 1-1 pick, and one of those can save you 1-3 million in slot money that allows you pay over slot later in the draft, you can have a significantly better draft class for the year rather than necessarily getting the one best player.
Consider last year Moniak signed for 6.1 saving the Phillies nearly 3 million of the $9+ slot. Likewise for the Braves signing Dansby in 2015 at 6.5 of an 8.6 million slot. It becomes a combination of finance, talent and need, and when you look at the difference of talent being slim between the top 3 pitchers and top 3 position players, the other factors weigh heavily. Now, when you have an unquestionable 1-1 like Harper, the talent begins to weight much heavier than the other factors, but there hasn't been that clear-cut 1-1 since him.