The weapons/items in the Randomization program have been given only to random enemies (no baskets or containers).
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My one hope with the randomization program is that it does not randomize things to parts of the game that are inaccessible in the same part of the game that you'd normaly be able to get the item. The staff of rynn, for instance, is normally available in chapter 2, so I would think it would be sensible to have it randomize to a chapter 2 enemy and not some enemy in the underdark, ToB, the asylum, etc..
From what I have seen in my game, I can tell for sure that weapons/items of the SoA part of the game will be given only to enemies of SoA and not ToB.
But this includes also the W.Keep (since it is accessible in the SoA part of the game).
Sikret could give more info about how it works, though one thing is sure: luck now is a very important factor in IA