Thanks for your feedback. The alignemt is a bit tricky, it is difficult to decide what to align with what. The custom offset number is the distance between the top of the page and center of the spread. Half of the page height centers the page on the spread - if you enter 0 into all of these, your tops are alligned, if you anter page height, bottoms will line up.
Automatic alligning of entire spread sounds like a nice feature we can add to the next update after 2.2 though, so stay tuned.