Given that they’re focused on reduction of waste and reduction of market fragmentation there’s definitely a question mark over only QI based charging.

I don’t see how you can get that from the text. The way I read it, wired and wireless charging are separate. There is nothing in the directive that mandates one should be used over the other. They explicitly require USB-C for wired charging, but do not put any requirements on wireless, as there doesn’t seem to be any significant fragmentation on the wireless side (i.e. no need to enforce a standard if everyone already agrees on a standard).