Question: Wouldn't Craft make more sense than Command in Know-It-All? Knowing how things were built would definitely help you craft something; there's nothing wrong with having Craft in two knacks since they do not stack; intelligent characters would have more support for certain common archetypes; many types of craft are more about knowledge than talent.
You raise good points, but no, we're pretty solid on Command and Craft where they are, the first in Know-It-All and the second in Jack of All Trades. The important distinction for us is that Know-It-All is only about things you know, while Jack of All Trades is only about things you do. Jack of All Trades involves being so quick on the uptake that you can fake your way through active abilities on the fly without having to know anything about them or have any experience beforehand; in that regard, it's actually the opposite of Know-It-All. Knowing things about what you're doing isn't what Jack of All Trades is for at all - you're doing everything by the seat of your pants, on instinct, rather than having any idea why at the outset. But it is what Know-It-all is for - Know-It-All can't actually do much of anything, but the Scion with it is so intelligent and so well-read that they know a lot of things that they can call up on the spur of the moment. This is why active abilities like Brawl, Craft or Stealth need Jack of All Trades, while passive knowledges like Academics, Occult or Science need Know-It-all.
Craft is almost always a very active ability; it's your skill in actually making or building things, and it's a must for Jack of All Trades (in itself it covers a lot of trades!). Crafting is literally working with your hands to make something.
On the other hand, Craft is not really a knowledge; the knowledge of how to do things with Craft is covered by things like Academics or Science, which Know-It-all excels at. Craft doesn't fit into Know-It-All any more than Brawl does; sure, knowing the principles of motions and human anatomical constraints would help you brawl, but that doesn't mean someone grabbing a dot of Brawl on the fly is learning force physics and anatomy at the same time, because those fall under Academics and Science. It's important to remember that while many crafts in the real world do require knowledge, they are not themselves necessarily knowledges; learning a whole lot about glassblowing technique will certainly help you if you want to be a good glassblower, but it doesn't matter for anything if you don't have a steady enough hand or the artistic talent to do it well. Knowledge is represented in Scion as Academics/Science/Occult and other related fields; it's distinct from the abilities that actually involve doing things.
On the other other hand, Command doesn't really fit into Jack of All Trades because it's not an active ability but more a knowledge of how to get people to respond and obey. Since it's an Attribute (Charisma) that actually puts the punch behind your commands, not an ability like Brawl, it falls more into the knowledge category than the action one.
Those who want to be a brainy crafter archetype are probably better served by picking up actual dots of Craft, and possibly Smith Among Gods, than they would be by fudging Craft into a knack where it doesn't belong. (Or even just getting Jack of All Trades, which only requires a single point of Epic Wits to get access to, after all.)
If we did allow Craft to be on Know-It-All, it would only be to know how to build a table - you still wouldn't actually be able to create the plans for the table or build the table, because Know-It-All is for knowledge, not doing;. You'd still need dots of Craft or Jack of All Trades to actually cause a table to come into being. So it wouldn't be a lot of help for the way you seem to be wanting to use it.
Honestly, I'm surprised that Craft was the focus of this question, considering that the two knacks have other abilities that seem to blur the lines to me more. Craft is definitely not one of the more ambiguous ones.