Each time once needs to use a clone from a backup, one needs to rename each file in the set of clones to not break references among the files. This can be time-consuming and error prone in solutions with "many" files.
This can be avoided by adding an extra option to FileMaker Backup Schedules > Clone the Backup file, "Do not rename cloned files".
Ideally, I would really have this be the default (or even only) behavior, but if it's better for backward compatibility, I'm fine with this being simply a new option.
Since cloned files are in any cased saved to a separate subfolder "Cloned_by_FMS_[Timestamp]", I don't believe there is a major risk of confusion if files aren't renamed.