But yes, the fact that the format is implemented as a ZIP archive containing audio files stored in one of several media container formats rather than as an application of an existing and widely supported media container format seems like a misfeature for a format that I assume most users will be more interested in playing than "unzipping".

And if the goal is a format that's easily editable with off-the-shelf tools, requiring the physically first file in the ZIP to be uncompressed with an empty extra field so its contents appear at a fixed byte offset seems counterproductive, when the stated goal of making the format easy to identify could be accomplished by requiring the manifest file to be stored first and giving it a more distinctive name than "manifest.json", given that the file name is the first variable-length field in a ZIP local file header and cannot be compressed.

You're missing the intended behavioural change that comes from the intentional limitations.

Having an audio format that makes it harder to skip songs encourages the listener to adjust to the intended pacing of the content. That's the point.