Emulator

Because of scoped storage on Android, I don't think this is possible.

Why?

It is possible. Enable Config > Paths > Search Subfolders for Game Files, then add the top-level directory for the game to Dolphin's game list. However, because of how SAF works (which we have to use because of scoped storage) this is going to be very slow. Assuming you're on Android 11 or later, the best workaround I have for that is to install an old version of Dolphin and then update it to a recent version of Dolphin (as described on https://wiki.dolphin-emu.org/index.php?title=Controlling_the_Global_User_Directory#Android) and then manually edit Dolphin.ini to replace the content URI to the game directory with a real path.

Can we have 2 versions of the app? One implemented through SAF another without. This way, we can still publish to Play Store while other users who want access to configs in dolphin (dolphin-emu folder) can download the APK here.

For example, Termux was not updated through Play Store because of what it violates Play Store's policy. Now, people download it through F-Droid or GitHub actions.

Similarly, we can have the Play Store policy compliant version of Dolphin pubished on Play Store and the non-SAF version through the internet (GitHub actions or provide 2 versions of Android Dolphin in downloads page).

This, however, would raise a new problem. Edits to the project will need to be applied twice and the code may have conflicts in the long run.

Nevertheless, I hope that there will be 2 versions of Dolphin (one SAF and other non-SAF) available. This can satisfy all users regardless of their needs.

If you want to, you can make your own local build of Dolphin where you just change the targetSdkVersion to 29. But I'm not sure if publishing such a build would be worth the resources used and the confusion caused by having two builds.

Also, the workaround I described really does work for disabling scoped storage, even though it's unintuitive. I would recommend trying it.