Hi @hazard.
WordPress only has one way of handling media out of the box. There’s both pros and cons to this. ACF itself isn’t really a content generating plugin nor is the main focus on front-end. It’s firstly a great GUI for meta data and a way to easily interact with advanced meta data (API). When it comes to the file/gallery/image fields ACF uses all native WordPress functions and thus treats anything uploaded the same way as if you would’ve used the core media uploader.
However I think with a bit of hooks into WordPress core you might be able to change the upload paths for specific post types. I found this post that might get you started:
http://wordpress.stackexchange.com/questions/95829/set-custom-upload-path-for-custom-post-type-only
