The mergerfs balancing tool causes data to be redistributed between the different hard drives in the pool. If you use that tool in this case you could end up with a backup folder split between several different paths. When you go to search for the path of only one of the hard drives, you would be missing files (because they have been moved to some other disk) therefore it would not be complete. So you should avoid using this tool to avoid that situation.
What ryecoaaron is referring to is that instead of creating a pool with entire hard drives you can create a folder on each of those drives and group those folders into a pool. That way you wouldn't have the problem you've raised in this thread. On one of the hard drives you can have the folder that is included in the pool and another independent folder for backups that is not within the mergerfs pool, therefore it would not be affected by the use of mergerfs tools such as balancing, for example.
I was completely unaware that it is possible to pool folders instead of drives. Guess I have homework now. You learn something new everyday. Thanks for the detailed explanation.