I believe in using whatever works. It does seem to me that what both babies are doing is not working for you. They've trained you.
I suspect you're worried that the baby won't get enough to eat if you set up the schedule and feed her less often? Perhaps one of the reason she isn't growing as quickly as she should is that by snacking she never gets enough to eat. I recommend talking with a lactation specialist.
By protecting her from distractions she hasn't learned to eat when there are distractions. And by allowing your son to interrupt, you haven't taught him to play quietly for 15-20 minutes.
You're concerned about leaving him in a room by himself. You can baby proof a room, give him a boundary with a baby gate, and reinforce for him that this is the way it is. I'd suggest you do this while not nursing. Get him started playing with several things available. Turn on the TV if you want. Tell him you're leaving and will return in 3or 4 minutes. Then leave and go to a different room. Return in a few minutes, let him see you, then leave again. Don't play with him. You're teaching him that you will return. Gradually extend the amount of time in between "visits" until he's able to be by himself for 10 or 15 minutes. Try to return before he begins crying at first.
He'll test you by crying. Be consistent. Return in the same number of minutes you've returned before. When you return and he's crying, don't make over him. You can get him started on playing again but no "you poor baby" type of interaction. You could say, "I know this is hard for you (name). I know you can play by yourself while mommies gone. I'll always come back."
Doing this is quite painful for parents. And perhaps a bit painful for toddlers tho they're never as upset as they seem or as Mom and Dad feel. They do need reassurance at the same time they're learning that they can play by themselves and you'll come back.
They will be learning things for their entire life. Teaching them to have success for themselves is a very positive action. When we don't give them the experience of sucess with reasonable expectations we are teaching them that someone will always bail them out.
I do believe in child centered living when the parent's needs are also included and the child receives what he needs but not necessarily what he wants.
Raising babies/children is difficult enough without making all of our decisions around the wants of a child. We want to raise responsible, compassionate adults. The way we do that is to balance our lives and needs with their lives and needs. Emphasis on needs. Over many years they learn to entertain themselves and to accept that other's are as important as they are.