My understanding is that the size of a run is consistent from Discraft to Innova, so neither one is having larger runs. Discraft just has fewer of them. Not sure what that does to the actuarial math for that probability. If it's anything like the conversations I had with my college roommate who majored in engineering, it means I'm wrong no matter what I say. Damn that Liberal Arts degree!
At any rate, I think the issue is perception of business practices more than quality control. When the high density plastics came out and it became obvious that the more dense plastics caused discs to behave more overstable in flight, Discraft did...well, nothing. They left their molds alone and released the discs as they were.
Innova, on the other hand, tried to account for the difference by creating "X" molds or "L" molds and essentially selling two molds under one name to account for the differences in flight caused by the different plastics. They also make decisions like making the DX Eagle in the "L" mold so there would be more difference between the flight of an Eagle and TeeBird, only to find out that it hurt their sales so they reverted back to the Eagle "X." That decision made a lot of Eagle throwers happy but also helps to confuse the average Joe who doesn't know the first thing about "X" and "L" molds. All the average Joe knows is that he bought one Eagle and it flew one way, then bought another Eagle and it did something completely different. Then he bought an XL and it did one thing so he bought another XL and it did the same thing the first one did. His perception might be that Innova has crappy quality control, when in fact he simply prefers the business practice of Discraft.
Myself personally, I see pros and cons to both approaches so I really don't think I'd call one company better than the other.
When you talk about the big rimmed drivers like the Wraith, Surge, Destroyer, Force, etc., there are big variations in those discs regardless of the company because those designs are so hard to mold up. I think the mis perception that Discraft has superior quality control should be debunked by the variety of Force you can buy, but that should not give any smug satisfaction to Innova since they can't make the same Destroyer twice.