I don't think (at least I hope not) designer's notes would be used for every feat and PrC, but for things that are a bit out of the ordinary. For example, the Mystic Theurge should have been presented with a small box saying "This might look broken, but it's not, because you still only get one action per round, you won't have access to the highest level of spells a single-classed caster will, and you'll have to spend resources (e.g. gear and feats) to keep up with two different types of casting." Similarly, the entire feat chapter in the PHB2 could have been presented with a box saying that it represent a conscious effort to make some high-level feats that are worthwhile at high levels, and the spells chapter in Races of Eberron could have included a box explaining the rationale behind those spells that give you some minor benefits while you have them prepared (can't recall the term they used for them).