I very rarely use align to parent as a main content layout, usually it is column or row. I use align to parent mostly on containers that are child elements of the main container. As such most all of my groupfocus elements are column. I put the close icon at the top, do the alignment on that icon to be right and I add padding to the left and right of the groupfocus for the spacing of all elements inside. I have not had any issues with my groupfocus design/alignment changing with the use of the custom css.
But of course, as you’ve seen it introduces a lot of other issues, and so might not be the best approach to use and may find more benefit from using custom code on a group to make it act as a groupfocus in terms of offset from a target element.