My daughter, at age 4 and 1 month finally started pooping in the potty two days ago. She chose a number of days and we did a countdown to no more diapers. The first days we discussed it, the number she chose was something like twenty-four-sixty-four-eleven-thirty--LOL. But one day she mentioned a countable number, 2, and I grabbed it. We kept talking about it, saying one more day, and discussing what mommy would say if she asked for a diaper after. The first day of no more diapers went smoothly. She was so proud of herself for pooping on the potty. The second day she was fearful that it would hurt. She had a little tummy ache and spent about 2 hours crying off and on for a diaper. I held her, empathized and was very clear that there were no more diapers. Finally, after a little bit came out in her pants, she went in and sat and amongst some more tears, went poop. Immediately the tears turned off and the smiles came out.
A little more info--We have been trying to potty train since she was 20 months old, off and on. She pee-trained at 3-1/2. She's known about her poop for a very long time, but we were having control battles for most of her third year, so I decided to let it go and let her do it on her own. Well, she turned 4 and still didn't want to go in the potty. Then once right before she turned 4, we were in a restaurant and she went poop in the potty there. She said she knew there weren't any diapers there. Aha, a clue that she just liked going in diapers but could go in the potty if necessary.
Her brother, who is 2-1/4, has been pooping in the potty since 22 months, 80% of the time. But, like your son, he sometimes misses it and is already going in his diaper before he tells me. He has no control over his pee yet.
Anyway, I'm sorry to rattle on about MY situation. I just thought it might help to know that this stage will eventually pass. My daughter is such a different person at 4 than she was at 3-1/2.
Unfortunately, I don't have any thoughts about how to handle twins, but your separation idea sounds interesting.