I’ve had the same problem for years. In my humble opinion, the lack of versioning is DevonThink’s biggest failing. As a long-term DT and DTTG user, I have entrusted most of my records to DT. I use Time Machine to back up the data, and I also perform a periodic dump of all databases which stored in multiple locations. But this is huge because every file has to be duplicated in each dump.
If DT came out with a paid upgrade (version 4?) which included versioning and verifiable consistency checking, like git, I’d probably run for my wallet to purchase the upgrade. Ideally it would be capable of building a full version history by stepping through years of Time Machine backups.
However, with several thousand critical files, I constantly fear losing something due to a system crash or a sync error from the bad old days of sync.
I would have liked to use git to checkpoint the databases on a daily basis because git guarantees that the checked files are complete and correct. It would allow me to go back to any arbitrary date and look at the database.
But alas, we have always been told that git is incompatible with DT. I have yet to find any other way to safely store all changes in a manner that can be interrogated (unlike backups), ensuring that no files are deleted or lost.