I think, there’s a chance machine-id could’ve changed. It shouldn’t on upgrade, but it certainly can on clean install. Another possible explanation is it’s indeed something else – an what I remember seeing is the same something else. Though again, what else can be put in /boot? And I remember subdirectories corresponding to kernels I’ve had at that time – exactly as you’ve described above.
There’s a common Fedora 30 bug that can be the reason (though it’s for BIOS/legacy i.e. non-UEFI systems), also we’ve had this case:
There the poster had corrupted grubenv file, and it looks like that prevented reconfiguring the grub to BLS mode automatically.