This is truly a change in behavior. I can reproduce what you are reporting. Namely, that your code causes the form to resize in XE2, but not in XE6.
To get around this, you can manually call AdjustSize:
procedure TForm1.Button1Click(Sender: TObject);
var
Panel: TPanel;
begin
Panel := TPanel.Create(self);
Panel.Parent := Self;
Panel.Top := ClientHeight;
Panel.Align := alTop;
AdjustSize;
end;