I can’t say I’ve got an authoritative answer, but this is something I’ve done a number of times without issue.
Aeon Timeline stores a timeline as a regular file, and Devonthink is friendly to any kind of file. I think it’s accurate to say Aeon is completely safe in Devonthink.
I don’t use Scrivener any more. It’s a great program, I got a lot of good out of it, and I keep an active license to support the effort. I’ve discovered Devonthink plus other tools is more to my taste.
Scrivener stores a project as a package, which is a directory of files and subdirectories. The Finder displays it as a single entity, unless you use the show package contents option.
Even so, I’ve never had trouble with Scrivener projects or other applications (like MindNode) that store output as packages.
Keep backups, but that’s always good karma.
The reason I keep work files in DT is to leverage DT’s sync features.
Fun fact - if you add custom metadata fields in DT for Aeon’s parameters, then you can do a pretty automatic export of Devonthink into Aeon.
Add metadata to Devonthink for start, end, duration, participant, observer, arc, and whatever else you want to track. As you add documents to DT, fill in the metadata.
Highlight the documents you want to export to Aeon. Use Tools->Create metadata overview in Devonthink. That makes a tab separated file of the metadata in your highlighted files.
Drag the newly created Metadata Overview document out of Devonthink to your desktop, or someplace you can find it easily. You could also use it in place, but it’s easier to find if you drag it somewhere.
Over in Aeon, use the import feature to read your tab separated values file. Associate the Devonthink metadata values with Aeon’s parameters.
No human intervention required. Devonthink to Aeon, on autopilot. The same kind of trick can be done with extra columns in OmniOutliner.