I have seen it written in a couple of locations that the Berthier 5 shot clips will also work in the 3 shot rifles. How can that be as they are longer?

The little tabs on the rear of the charger is what holds it in the magazine held by the charger latch and these are of equal distance that allow either the three round or five round chargers can be used in any weapon.
Here is an example:
Nota - Bien que le fusil ait été modifié pour employer un chargeur à cinq cartouches, il peut utiliser les anciens chargeurs à trois cartouches. "Note - although the rifle was modified to use a charger of five cartridges, it can use the former three cartridges chargers.
When using 5 round chargers in a three round magazine it sticks out a bit but will not affect operation of the charger at all.
If you go to this post you will see the original line drawings of the chargers and this will give you an idea of tab distances.
viewtopic.php?f=148&t=61783
Patrick