I've seen this for years with POD books. You can order a batch of 5 copies of the same book and get very different alignment on each cover, all printed at once, using the same cover file, and arriving in the same box together. It's random and has nothing to do with the files you upload, just the individual printing of each book. If you're already following the print template, all you can do beyond that is use a design that blends as seamlessly as possible around the spine so that if/when they don't align it properly at printing, it won't look terrible. Then you cross your fingers that you'll get good alignment more often than not. From what I understand, it's to do with the machines and the way they handle different sizes.
I'm not saying it's definitely unrelated to the migration. It's possible that they've adjusted the files in some way, adding to the problem. It's just that I've seen it on Createspace and KDP Print books equally. You can adjust the files on your end all day long, trying to compensate for the low quality of the physical printing on their end, but inconsistent printing is a known problem with POD.