The squat and bench thing is imo only partially right. I think as long you are under 300 squats and bench can't really hurt you and it is the quickest way to get stronger.
Now if you bench or squat 400+ it might make sense for a pitcher to be a little more carefull with those exercises due to the shoulder stress but as long you are under 300 just lift your butt off to get stronger, it simply doesn't make sense to do single leg bosu ball squats when your max is 170 in the squat.
Regarding the program it honestly doesn't matter all that much as long you increase your weights.
There are a lot of fancy training stuff but I actually like a classic periodization which is like first doing a bodybuilding phase were you do a couple sets of 8-12 reps for a couple weeks and then when you stop progressing you add more weight so you only make 5 or 6 reps and then you go really heavy after another couple weeks with really short sets.