Took a quick look at how multi-root workspace works (https://code.visualstudio.com/docs/editor/multi-root-workspaces), you could create a separate dendron workspace, add all your projects to it with

Add folder to workspace...

in the explorer, and have each of the "roots" have their own settings scoped to the respective projects (they go in the

.vscode

under the project: https://code.visualstudio.com/docs/editor/multi-root-workspaces#_settings). A bit of work moving the individual workspace settings to a folder setting, but this way you can preserve most of the project scoped settings that matters. and of course have one and only one place where the document is stored / synced