I believe it does. For example, Zeus has an ability that says to skip his play phase which means he cannot put warriors or Disciples into play. That pretty much means he cannot buy during the recruit phase since he will have no Faith points.
So, I think the order does matter and should be done as written but sometimes it may not matter as you may not be doing anything that is affected by the order.
Yea, because the first couple times I played, I kept buying cards to put on top of my deck and then use an adjuction to always get the right card