You are correct and thanks for pointing it out. I hope this doesn't make people get scream and shout... let me explain my logic:
1. All .{lmdb, tcdb, qdbm} files retain persistant state, not just a select few. Placing them all in the same common, top-level directory enforces coherence... and configurability now.
2. Most--but not all--internal CFEngine writes happen agains the embedded DBs. This change effectively isolates those writes. One use-case: constrained embedded devices whose filesystems are [primarily] backed by flash-based storage.
3. I've seen references to state files being scattered, the most recent I can find is cfengine/masterfiles#105.