I find the alignment tool good for many but not all instances similar to the challenge described. In those instances I have become a fan of using the property panel which is on the far right of the tool bar. There is a field showing Left and another for Top. I will simply enter value. It is not as fast as align but works well. I will also use to help with spacing as it also have fields for width and height. So when spacing an array of buttons or indicators you can with a bit of math get your spacing precise.