Where are Gold Boxes from from?

Mistaken understanding here; There are two types of monster drops, explicit and scripted.
Explicit are in the actual drop table, manually entered mob by mob.
Scripted are triggered by events. Monster cards for example are scripted. They don't show up in the drop table. The original monster cards that every monster had a chance to drop were as well. Most events like this are as well.

So apparently the monster book only shows explicit drops, not scripted ones, which isn't that surprising really.

That makes sense, and also supports my vague impression that sometimes it takes a few kills to "prime" the script before you'll start seeing special drops.

Which sucks when you're trying to get a monster card from Homunscullo, and it's taking days on end to even see one spawn.