Option for missing information

The plugin system that does the duplicate detection takes the entire Media object. You'd be able to write a comparison plugin that addresses your needs and use that instead of the default.

At that point, the standard duplicate detection response would kick in. It doesn't give you all the options in your issue, but it does tell you which media item is conflicting, so you can go an update it if required.

Does this solve your issue?

I'm not sure. Here's a better specific use case scenario.

1. A user takes a picture of themselves on a mountain. The image has geolocation data by default.
2. The user uploads the picture to a private or cloud storage that strips metadata.
3. The user then uploads the photo from their storage to their Drupal site. This image has no geolocation data.
4. The user then decides they want to create a map for the pictures that relies on the geolocation data, so they re-upload the originals directly from their camera.
5. The duplicates module detects the images are the same.

In this case would it in fact detect them as the same, or would the missing metadata make them unique to the module?

Out of the box they would be considered duplicates. But you can write your own plugin that would take into account both the file hash, and the geolocation data.