(1) When I refer to standard form elements, I am actually referring to two separate things: the standard interaction for this particular type of option and the native element for supporting that interaction. I believe your argument is that we could have made custom elements that supported this standard action (e.g. checkboxes) that may have performed just as well or better than the native elements. While this is certainly possible, the point was intended to be more about the standard interaction and less about the native elements. Of course, the native elements are nice because they support these standard interactions and they are easy to maintain.
Although it wasn't shown in the blog post, the faux selects used (custom) checkbox buttons for selecting multiple options once opened.
(2) I originally intended to mention this, but ended up cutting that paragraph. As you point out, the faux elements were designed to save space, which is why they didn't have labels. Part of the standard form interaction is having the labels above elements, so that's what we did. However, in retrospect, I wish we had tested the label and element changes separately. I suspect each of them would have shown an increase in conversion.