Is it worth it? Leaving baggage reconciliation aside (already discussed) there are many reasons why containerisation is a "very good idea"™
Rather than four manual steps (load onto trolley, unload from trolley, load onto trolley, unload from trolley) there are two (load/unload container). Activity is mostly indoors, out of inclement weather, and can be more easily monitored. Less handling means less possibility of damage to handles, wheels, etc
Bags don't fall off a container as they do from trolleys.
On common connecting routes entire container can be connected. And baggage crews can know well in advance which containers contain connecting bags, and to which onward points. Low minimum connecting times (LX's 45 minutes at ZRH) simply couldn't work without containers.
And then there is freight ...
Of course not all of these benefits apply to all business models. LCC don't see advantages for them and don't use them.