Questions regarding add_meta_box()

To answer #3, just search ACF’s input.css file for the class no-box and you’ll see how it works. If you view the meta box in the context of the edit screen, and delete the no-box class using your browser’s web inspector, you’ll see that it will appear as and can be sorted like a normal meta box, so it is entirely CSS that does this.

The important bit is to hide the meta box title h3, which is the element that makes it draggable.

.acf_postbox.no_box > h3,
.acf_postbox.no_box > .handlediv {
    display: none;
}

The rest is just styling to remove the background, border, and adjust margin/padding.