When done properly, the bench press recruits many more fibers than any isolation exercise could (I.e. flys) for the chest. Furthermore, compound movements stimulate the release of more growth hormone, and the load will stimulate osteoblasts to build thicker, and denser bone. Compound movements save more time in the gym, and allow you to pack on those plates, which you can't do with single joint movements. I would say if you are experiencing rotator cuff issues it's most likely due to a muscular imbalance., or possible history of injury to one of your rotator muscles (probably external). Also, a very common mistake is to flare out the shoulders, which taxes the delts and rotator cuff much more than tucked in elbows. You will find that you may do less weight, but it will do less wear and tear on your shoulders in the long run (especially with heavy loads). I suggest reevaluating your form if you are having rotator cuff issues, or if you fear you may in the future. Also, try warming up with some external rotator movements. You should be able to move 10% of your bench press weight for atleast 10 reps during an external movement. If you fail to due so, you're benching too much for those small rotator muscles. Your biggest lifts are only as strong as the weakest link in the chain.
As someone with a Massage therapy and bioscience background, I applaud your in depth analysis of this.
That said, just because you're doing a bench press or an incline press doesn't mean you have to use 300lbs or max out your weights. If you've got weaker triceps/biceps like I do, you can go below your weight max.