It seems we have a concept of external/default extensions that are not supposed to be synced. See https://cs.chromium.org/chromium/src/chrome/common/extensions/sync_helper.cc?l=36 . The following repro steps use how by having the Google Drive app installed, we set Google Docs Offline extension to having been installed by default.

1. Use a clean-ish profile/account that doesn't currently have either of these apps/extensions installed.
2. Sign in and start syncing everything.
3. Install extension https://chrome.google.com/webstore/detail/google-docs-offline/ghbmnnjooekpmoecnnnilnnbdlolhkhi . At this point, sync will record that the extension is installed and various state about it (most interesting if it is enabled or not). You can view this at chrome://sync-internals > Sync Node Browser > Extensions. Toggling the enabled status at chrome://extensions/ will cause sync to send out commits which can be seen on sync-internals.
4. Install app https://chrome.google.com/webstore/detail/google-drive/apdfllckaahabafndbhieahigkjlhalf
5. Restart Chrome. On restart it will set Google Docs Offline to think it is installed by default. This will cause extensions/sync integration to stop writing changes.
6. Toggling enabled status no longer causes commits. Go to chrome://extensions/ and disable Google Docs Offline.
7. Restart chrome and notice that Google Docs Offline is enabled again. This is because MergeDataAndStartSyncing still writes sync data into extensions on startup.