On the subject of Urobuchi "getting it right" in Zero and HA wishes:
Spoiler:I was under the impression that they were referring to Avenger's possession method, not the wish granting mechanics. They way he replicated and took on the form of Iri while it remained "truly her," or whatever being the same thing as how he takes on Shirou's form.
As for Wish Granting in HA and why it doesn't destroy the world, the way I heard it explained is that the "wipe out the world" bit only happens if the GRAIL grants the wish because its functions have been corrupted, just like its summoning functions were corrupted. After all, Avenger isn't the one summoning broken glitch servants, he just polluted the grail so it could, and the "all wishes equal death" is the same thing, NOT Avenger's personal will or anything.
In HA, its not the GRAIL granting Bazette's wish, which is why everybody doesn't die. Rather, its Avenger himself, because his nature as a heroic spirit is in fact the fulfillment of wishes (ie, the wish by his torturers that he bear all the evils of the world so they could be pure.) I can't say I know WHY Avenger decided to grant her wish though. That's just the summary/explanation I've heard.