There are obvious potential cons to a trigger-happy lifestyle with mods—textures breaking and forming horrendous-looking characters and other general bugs (which, even glitches are arguably enjoyable)—but I had never considered Errant Signal's discomfort with them; namely that mods break what was supposed to be the game's original, shared universe.
But if you watch his video above (and skip to about 48 seconds in to get to the good stuff) you'll see that Errant Signal comes to terms with this idea and even suggests that the malleable nature of games actually becomes a part of that universe.
That's always how I've interpreted them, too. It's an expanded universe, with more input from a potentially infinite number of creators. Some of that will be noise, of course, but a lot will enhance the game's experience in a way you'd never know of otherwise. And I'm reminded by that every time clips of the Thomas The Tank Engine mod comes up and I can't help but giggle.