FYI, here’s what I see on MacOS 11.6, Numbers 11.2, and DEVONthink 3.8 …
- Drag a fresh Numbers spreadsheet into a DEVONthink Group in my Works in Progress database. I confirm I am working with a Numbers file in DEVONthink and not one still in the file system.
- “Open With … Numbers” that file as I point to it with mouse inside DEVONthink.
- Make a change. In Numbers Menu File → Close, and the file is saved back into DEVONthink. Numbers does not ask permission to save. File saved back to DEVONthink with changes.
- Numbers spreadsheet is then nicely displayed in the DEVONthink window
If I do a “Open With … Numbers” again, then make changes, and say Numbers Menu → Save, the sheet stays open and a new version stored in DEVONthink. Same with Command-S save key.
So, I’m not seeing what you report. I’m not running any beta software.
I’ve been exercising Numbers recently to see if I can drop my Office 365 license in January when it’s up for renewal. So far I conclude I can.