General suffix-application mapping only works to a limited extent under Sequoia

FrankEbeling wrote:

Since macOS Sequoia, it seems that all applications must be stored freely in the "Applications" folder and can no longer be moved to an Applications subfolder as before, for example, to neatly organize all audio applications in an application folder named "Audio."

There has been no change. It's just that applications are special. They are managed with an internal database. If you move the apps around, then the internal database gets corrupted.

Usually all you need to do is manually launch an application after moving it. That should update the internal database.

The general mapping of suffixes to applications no longer works, or is not retained by the Mac.

That's the same database as above.

Regardless of whether the files are WAV, AIFF, MP3, or MP4 files, when I open this file type, the Music app still opens.

Aren't those all music files?

The mapping of the suffix to the application via the file information is no longer saved, and audio files are blocked with the following security message:

"Apple could not verify that 'ABC.mp3' is free of malware that could harm your Mac or violate your privacy."

That sounds like something different. It sounds like you downloaded those files using a 3rd party app, and then moved that app. So the files are now tied to app that is considered lost. Hopefully it will work once you manually launch that app.

This is a security issue. Suppose you have your favourite app set to open all those files. Then you "download" an "inexpensive" version of some professional app via Bittorrent. Little do you know that this app includes some "helper" apps to take over all your existing documents. So when you double-click one of these documents, it's going to warn you because it thinks some other app has taken over these documents and you haven't authorized that. When you move apps around and break those internal database pointers, that's exactly what's happening. You have to clean up the mess before you can use the system normally again.

The error doesn't occur with image files such as JPG or PNG files. There, I can select Affinity Photo, for example, as usual via File Info > Open with: "Assign an application to each file extension so that all documents of this type open with this application" > "Change all...", even though I had already moved it to the "Audio" application subfolder after a restart.

Most likely you had accidentally launched Affinity Photo manually and pre-fixed that one.