Late last year I flew aaa-bbb-aaa-bbb-ccc-ddd across Europe, all in one day, for exactly that reason. Five flights across four separate bookings/tickets. The connection at ccc was the tricky bit, not only "connecting" on a different ticket (so not really a connection), but a different airline alliance.
They design the system, you follow the rules. Unintended consequences aren't really your problem.