Ah, interesting, and a good catch! The way the Mishap section is worded does seem to support that interpretation (and it makes an amount of sense too).As for the "do dice even exist" metaphysics discussion: there's one place I can think of where it matters, which is mishaps. If you do not have the relevant skill at all, then rolling a single mishap result counts as a mishap. If you do have the skill, though, and the die was simply modified out of existence, then you still need to roll 2 mishap results to get hosed.
Can one of the developers comment to confirm/deny? There is a little bit of weirdness introduced in that someone with a D rated skill who gets a -1 modifier can then never roll a mishap (unless they're shooting and using ammo dice), but someone who is better in the same situation still can roll one, which I'd have to ruminate on for a bit