The USGA Handicap System four ball handicap allowance is a recommendation. My experience is that one of two thinga actuall happen: 1. all players take all their strokes, or 2. there is some negotiation before the round.
There two ways to look at the issue. Either it's too bad that most people don't folow the USGA recommendation because it is based on research and found to be most equitable, or, since so few people actually keep handicaps properly, the recommendation makes no sense.
I am not aware of any other formal system for four ball handicap allowance. I suspecgt some clubs have systems which have developed over time and become traditional.