I don't buy into the idea that any ONE workout will be best for every possible application. But that is what makes fitness, everyone has their own view on what does work. Boyle probably doesn't think Chek is right all the time either. It's the flexibility to learn and adapt as neccessary. Even CF is a program that changes their WODs as they learn more about what works for their trainees. (as now you see more heavy lifting days for example)
Just like no one program is best for every possible application, so is everyone and their specific needs/imbalances/weakeness/injuries prevention different. It would make no sense for an athlete that has muscle imbalances to jump right into a full program of complex lifts without trying to fix a foundational problem. Much like an offseason program should be programmed differently than in-season workouts. (for athletes) All full body movement programs that use compound actions and varible free weight resistances will be of benefit for any athlete. So no need to say one program is the best...you take the best exercises for your needs and apply them. Have a CF metcon day, have a 5x5 strength day, have a Boyle sports specific day, have a yoga recovery day....training is taking what works best for you and applying it.