Images are uploaded via ajax using the core WP uploader -- which is why they end up in the wp-content/uploads folder.
You can filter the file name:
And filter the upload folder:
But... my guess is there's no context as to which ACF field that file is being uploaded to -- since core WP doesn’t really care where an image is being uploaded.
All uploads, sure. All PDFs in a separate folder? Sure. Use /uploads/a/ vs /2014/? Sure.
Your case is trickier.
The only way I could see this working is an update_post_meta hook (that has the context of which field it is) that moves the already uploaded file (if necessary) ... then regenerates the media metadata so WP doesn’t look in the wrong place.
So, it's possible, but it'll be a bit of work.
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Nick Ciske
@nciske