I agree with you that the Elements Backup/Restore process is not efficient for a large catalog like yours. My catalog now has almost 300k media files and I have used other backup systems for many years.
I simply use different external drives to copy the media files. I then use a file-synch utility to update the "backups". As for the catalog itself, I just copy the catalog folder to other locations. However, because the folder contains hundreds of thousands of small text files, I will zip/compress the folder before copying it. This saves a significant amount of time, even when taking into consideration the zip/unzip process because one large file is exponentially faster to copy than thousands of small ones (at least on a Windows system - I know nothing about Macs).
The only possible problem I see with your system, where you have the files in various locations, is that if you need to recover/restore the backups, they must be placed back in the original folder structure. Otherwise, the files will become "missing" in the catalog and will have to be reconnected - which is a time-consuming process.
BTW, I also don't use the automatic folder structure backup frequently. But you can never have enough backups!!
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