Is there any point in keeping knowledge systems separate?
No. Once you master contents categories and templates, there is no point. You gain global search, global registries, global repetitions, global optimization, etc. This would not be advisable back in SuperMemo 7 as item difficulty measure (E-factor) was dependent on the average difficulty of items in the knowledge system. Presently, the item difficulty measure (A-Factor, or absolute difficulty factor) is absolute and does not depend on the context in which an item is placed. Only the length of the first interval will significantly be affected by the average difficulty of items in the knowledge system. However, this shall not bear dramatically on the speed of learning. Especially that variable forgetting index for individual items makes it possible to set different first intervals for whole contents categories or branches of the knowledge hierarchy.