The retcon is that the whole spore drive program was actively suppressed, because any knowledge of Discovery and/or Control would lead to cosmic apocalypse. And so part of Section 31's imprimatur was to work behind the scenes and prevent it and other disruptive tech from seeing the light. And other civilizations did the same, because the same thing happened to them at some point in their history.

It's pretty sweaty, and requires quite a bit of stretches credulity, but it beats a lazy handwave.