This is just my experience but I've found that if I have a neat set up that I don't want drifting around after multiple saves (or even sometimes just exiting the material room or switching materials) If I save an mt5 of the setup and reapply it seems to make the arrangement "stick". Unfortunately this doesn't seem to work for material collection files.

For scripts I use an align nodes and a Root Default pos value script that ADP made for me as a python request.