Five-round chargers are far more compact, for one thing.
The main reason is well-expressed in the Canadian Army training manual for the #4 Rifle, when it states that standard procedure will be to add a five-round charger-load to the magazine whenever its contents fall below five rounds. This is one MORE big advantage of the Lee Enfield-type rifles over the Mausers and Springfields, etc. The magazine does NOT have to be empty before a stripper or charger can be used to replenish the ammo supply in the rifle.