One Suggestion: When I have a bunch of objects selected and I choose to align them I think it should probably keep the selected elements relative position to each other and apply the alignment to the entire set of elements vs applying individually to each element causing them to smash up if they are on the same horizontal or vertical axis.
To get the behavior you desire, you could group all the elements together and then move that group. The alignment option is specifically for aligning all individual elements to one particular baseline. Like for example if I am building a form and want to align all the fields in the form to each other, I would select the fields and then align them to selection left.
If I have misunderstood your comment, could you please elaborate a bit?