It sounds like your trying to do too much hacking with the core functionality here. Uploading to a custom folder would actually be messing with WP’s system, not really ACF’s.
I’d recommend you leave the system as-is and just grab the gallery images in your template file, creating the CSS on the fly right there. You wouldn’t be able to place this CSS in style.css but you’d have the ability to adjust the images from the gallery field and maintain the flexibility you want.
