Hi Dominik - my answer would be: it depends. I think you're on the right track in thinking, but let me elaborate.
Before I elaborate, let me throw out two caveats: 1- I love reading Eric Cressey's stuff and think he's doing great things to advance the landscape of baseball strength & conditioning; and 2 - everything below is my opinion and personal belief based on learning as much as I possibly can about baseball strength & conditioning in order to be a better baseball strength coach. I very much have an open mind and want to hear other opinions, especially those that differ from my own.
So, it depends. The reason I say that is because I view strength training as a pyramid. You have a base and have to build up from there. You don't work on things at the top of the pyramid if you have deficiencies at the base. The pyramid I'm thinking about has 4 tiers.
At the base of the pyramid (remember my caveat #2, just my opinion) is general physical preparedness. How athletic is this player? How does he run, jump, perform bodyweight exercises like pushups, pullups, bodyweight squats, etc? Do they move their body athletically? A 10 year old that is a super star at baseball, but hasn't ever played any other sports, may have some work to do to balance out their development from a general physical preparedness standpoint. A high school multi-sport athlete may have great kinesthetic awareness and have this base covered before setting foot in a weight room.
Next comes the general strength base. Deadlifts, squats (back and front), cleans, pressing (incline and *gasp* overhead!) and pulling (barbell rows, weighted pullups). Again, this is just my opinion, but a typical HS baseball player can live on this tier in the pyramid for their entire HS career and still make steady continual progress. As a very general (perhaps overly broad) rule, even for an athlete squatting 315 to full depth, adding 25 pounds to your back squat will help with sprinting ability. The fact that more force can be applied to the ground trumps any fancy agility ladder drills.
With a good strength base, the next level of the pyramid is more sport-specific exercises like you mention. For baseball players, this would be the rotational work with med balls. Eric Cressey trains a lot of MLB guys, so he can have his guys focus on these movements. You have to walk before you can run - so, if you're deadlifting 150 pounds, focus on the compound lifts before you dedicate 90% of your weight room time to med ball throws.
The last tier would be even more specific to movements of the sport. I haven't given this tier too much thought, and not even sure what I would include here for baseball. Agility ladders? Like I said walk before you run. Most baseball players can be in the middle two tiers for most of their career and make plenty of performance improvements.
Sorry for the long response, but I'm writing an article for my website on the strength & conditioning pyramid for baseball players, so it was a natural reply that just needed to be copy/pasted.