Each player has 13 skills you can influence by training and I see no reason why managers, who refuse to train FT, should benefit from doing JR/JS training.
But the way that training program is already set up kills your argument.
If I choose to never, ever train JS directly I can still train it indirectly by training JR, IS or 1 on 1. If I refuse to train blocked shots, it will still be trained indirectly through ID.
All the training skills already set up to cross train the other skills indirectly except for FT's (I would say stamina too, but that's not actually a skill).