Restore ENTIRE system ROOT / (CLARIFICATION)

I recently had to restore the disk with **borg**. So via live linux, I entered my disk file system, deleted everything (root **/**), and restored a backup of a specific date. *Now I ask myself:* **do you need to align the disk or the files?** (*inodes*, etc... in this case, some *inodes* have also changed). That is, I know that some files (mainly system files) cannot be copied normally with the classic "cp". In this case a "cp" command was not used but a copy was made anyway. Don't the files have to *"move them to the beginning of the disk"?* Is there a difference, in this case, between a **HDD** and an **SSD**? (my system is on ***SSD***)....and, can i copy the system with the classic **cp**? I would like more detailed explanations on this. Thanks and apologize for my english.