The effect of vorpal, itself, is what I was characterizing as 'meager.' Increasing a die size - like the Rogue does with Shuriken, for instance - brings it up a full point, and is actually a bit more significant.
Yes, 2d weapons get twice the benefit, but, as you acknowleged, they're already statistically different from 1d weapons in other ways. If you go the other way, and penalize 2d weapons, they get only a fraction of the benefit. You're not getting parity either way. And, even among 1d weapons, you don't have parity by any measure.
It's just not the kind of mechanic where how balanced it is aplied to certain types of weapons is a big deal. Yes, you get the most bang in terms of average damage from a 2d4 weapon - if there was a 3d4 weapon, even better - but, even from those weapons, the effect of Vorpal isn't overpowering. On average, wielding a +6 vorpal falchion dishes out slightly less average damage than a +6 Maul. NBD.
Honeatly, no. 'Per die' seems like it should mean 'per die.' D&D has used per-die modifiers before, as did other old T$R games, and it's always meant 'per die.'