We've a few rules we use for external file storage.
First we change File -> Manage -> Containers menu from the default [hosted location]/Files/ to [hosted location]/FileName
The reason for this is that we got caught out when adding encryption at rest (EAR) on a few hundred files spread across out customer base. If you have a separated or multi-file solution and leave the default settings, then it is almost impossible to add EAR, as EAR will fail unless it has access to all the externally stored files (EAR will also report failure if a file is missing, but that's another story).
Hosting on FMS using the default is fine, as the RC_Data_FMS folder adds a file name ahead of the 'File' folder, but working locally, as you have to do with EAR, it requires the folder name given after the [hosted location] to be in the same folder as the file. This also helps using fmDataMigration or just uploading using File -> Sharing -> Upload to Host. You cannot just take a backup with the RC_Data_FMS folder, or the folders at first level within this (file names) and upload this way, using the default settings you have to have the extenally stored files in a folder called 'Files', hence in multi-file/separated solutions you're in trouble as you can only have 1 folder called 'Files' for all your .fmp12 files.
As for the Container 'Store container data externally', if you're using 'Secure storage', this sorts itself out. However, if using 'Open storage', we always enter:
Year ( Get ( CurrentHostTimestamp ) ) & "/" & Month ( Get ( CurrentHostTimestamp ) ) & "/"
This gives a folder for each year, with up to 12 folders from 1 to 12 for January to December, hence each subfolder only contains 1 month's worth of files. This has worked very well for us over the years and avoids the problem you mentioned in your original post.
We came across a new client recently, who's incumbent developer had set the open storage settings based on the key field serial number. They had a folder for every single record for every table containing a container field!
We didn't realise how important it is to get external storage setup correctly until GDPR forced us into EAR, the default settings increased the time it should have taken by an unbelievable amount, as the impact is not apparent until it is necessary to take the hosted files and work on local copies.