I'm not sure I understand. Why is it a contradiction for something with an angelic recipe of 100 lines to generate something with an angelic recipe of 1000 lines?
The angelic recipe is the shortest recipe that produces the thing. So, if something has an angelic recipe of 1000 lines, it cannot be produced by any shorter recipe.
The problem with the Innovator is it creates a large collection of objects that must in aggregate have a larger angelic recipe than the Innovator.
The part that might be confusing is the second step of running the Innovator to produce the collection. But this would just be one more step added to the Innovator's recipe.