The App Store edition follows Apple sandbox and review requirements. The direct edition follows its own signed distribution and update process.
Why features differ
A tool that requires system behavior unavailable to sandboxed apps may appear only in the direct edition. Do not assume a missing tool is broken.
Why permissions differ
The App Store edition can ask you to select Home and save folder authorization. The direct edition does not use the same Home-selection flow, but macOS privacy controls still apply.
Why updates differ
App Store releases are installed through Apple. Direct releases use the supported Doinno update path. Release timing and version numbers can differ.
Switching editions
Install one intended copy in Applications, review permissions again, reproduce preferences as needed, and start new scans. macOS does not automatically transfer every permission between separately identified copies.