Since Safari 15, the extensions local and sync storage seems to be merged into one. This means operations in local storage apply to sync storage and the reverse.
This caused the users of of my extensions with more than half a million of downloads to loose all their user settings.
To keep compatibility across browsers, the sync and local storage should be separated.
A sample extension can be found here: https://github.com/carlosjeurissen/webext-tech-demo-extensions/tree/main/issues/safari-9723963-merged-sync-and-local-storage
And the feedback assistant report can be found here: https://feedbackassistant.apple.com/feedback/9723963
Thanks for the report! We are working on this.
It appears that as of Safari 15.2 (or 15.3) and/or macOS 12.2.1, this issue (along with several other Storage issues) is resolved. Here is an example demonstrating that "local" and "sync" have different contents
(I've omitted the code that got it that way because it should be obvious).