Again, the evolved undead example doesn't apply.
Unlike the evolved undead template, what we're doing is not just stacking the same template multiple times, we're "buffering" it with another template that makes the previous one "pointless". THAT'S the big deal. The logic is similar to any legal loop in D&D, like the Consumptive Field loop. Technically, you shouldn't be able to stack the effects of a consumptive field on another, since they are the same effect, but the effects of one at a greater strength supercedes the other, and enables you to go further. The same thing happens here - once you apply Incarnate Construct, the creature ceases to be the same that it was previously (type change), but that doesn't mean it didn't go through a change that made it stronger (Dustform was applied). And once you apply Dustform again, the creature ceases to be an incarnate construct.
I believe there was mention of using a loop with a thought bottle and becoming an evolved wraith that allowed you to effectively become an "ECL 20" character with tons of feats, HP in the four digits, inanely high saves and every class feature known to man. Similar principle there.