Benefits of storing uploads in an assets folder?

The only directory a theme or a plugin should write to is the uploads directory. That is the only directory with guaranteed write access (besides the server’s temporary directory).

Anything else is wrong and might not work.

There is no practical difference between both, except one: the upload directory may be on another (sub) domain to save HTTP data. Cookies aren’t sent to other domains, so an upload directory inside of the WordPress domain might be slower.

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