Writing notes by topic can get in the way of understanding
Partitioning notes by topic can isolate knowledge, and isolated knowledge stops growing. New meaning arises when a note meets other topics, and splitting them by topic in advance blocks that meeting.
(“Splitting by topic” here means confining the content of notes inside topic partitions, which is a different layer from top-level folder classification such as PARA.)
So do not isolate, connect — Link notes whenever they touch, even slightly. Related: Learning is understanding, not remembering — isolated knowledge fails to grow because understanding comes from connection.