Unfortunately this would be a feature request that would need to be brought up to Adobe, since the alert messages are brought up by Extension Manager. When it is installing and runs into a duplicate file, the extension manager will ask if you want to replace the files, not the extension itself, so we have no control over how the messages are displayed or if a button to replace all older or all newer files will be implemented.
From our testing, as long as you are installing the newest updated extension, replacing the files will not cause any issues.