Right, a manufacturer can't be allowed to hold an advantage over the field due to "unfair" design improvements! They must install restrictors and limiters, and carry extra weight.
If the organizing bodies could limit competition to "2-strokes only", the European brands would have to go away and leave motorcycle racing to the Japanese. So we must conclude that emissions standards haven't been entirely anti-competitive, although the fact that they allow Ducati to stay on the roster is an unintended consequence.