I had this issue with my younger son --- he will be graduating from college in the spring and, contrary to my fears, is not still pooing in his pants! :o)
My son was well over three when we had our "breakthrough." When he was that age, there were no pull ups. Believe me, I would have used them if they were available! And it would have made me very happy if he had asked me for a diaper and waited until he was wearing one to poo -- what a mess!
I believe, with some children, it IS a control issue, but I don't believe that's the case with all children, at least not in sense that they want to control this situation. I tried EVERYTHING with my son -- rewards, punishments, pleading, etc. Nothing worked, in fact, it often made things worse. He wanted to go to preschool and I told him he couldn't go unless he poo'd in the potty (which was actually true). Didn't work. Finally, in frustration, I gave up. Decided that he could figure it out in college. :o\ He knew it didn't make me happy when he went in his pants (from previous attempts) and would go days sometimes between bowel movements. Other times he would hide behind doors, etc. (Even after I stopped reacting to it.) Then a few nights in a row, he went in the bathtub during his bath --- ACK! But after a couple times a lightbulb went off in my head. He just can't RELAX to go on the potty! After that, I watched him VERY closely in the bathtub and when I saw the tell-tale signs, I picked him up and put him over the toilet and held on to him. It was a little difficult for him to stop "mid-poo" so.... HAPPY DAYS!!! He went poo in the potty! After this happened a couple times and he realized that he wasn't going to fall in or anything (yes, I was using a child sized seat for the "big potty" and also had a potty chair in the bathroom) he was able to relax and go. It really was that simple.
I believe, with boys, it is a little more difficult because they can pee standing up (which was the only way I could get him to pee in the toilet.) I think girls learn earlier to relax while sitting on the potty, because that's the only way they can use the potty. I don't know if using the diaper on the toilet would have worked in my situation, but I think it's an interesting concept and worth a try. I also think half your battle is solved since he will TELL you when he has to go (mine didn't.) Try working the relaxation angle. Whatever relaxes him - bath?
Mostly, I wanted to write and tell you to hang in there. Try to relax and believe that this is a temporary problem. I promise, he will not be going to his college graduation in diapers! =)
I am the 47 yr old mother of three grown children. Two boys and one girl.