I am having trouble trying to set boundaries; specifically, is there a way to make her understand that my hesitancy to support (or even just not object) to her plans centers mainly around the effects on our kids.
Therein lies one of your biggest problems if she is considering the two of you S.
I think you need to give up for right now in trying to make her understand anything from your POV. It will to a R every time and end in an argument. She probably has her heart closed to anything you have to say at this time. However, that is no reason to allow her to dictate to you how or what the children will do. This is probably going to be a very tough area.....especially living under the same roof while S. The kids are exposed to their parents stitch. Try to not show any anger toward your W or say anything to the kids in a negative way about their mother. It would be good if the two of you could reach that decision....but again, she may not listen to reason.
As the man in the family, you need to make your statements with "I have decided....." whenever you are setting boundaries. It shows strength and leadership. Be prepared to enforce whatever you set as a boundary. If she does not respect you, then she will fight you where the kids are concerned and test you to see if she can bully you. I hope you will not misunderstand how I mean this statement of saying "I have decided". You do not want to appear that you are bulldozing over her, but to make a stand as the man in the house. In the past, if you have given over to whatever she has said goes regarding the kids.....then this will be something new to her! Be armed and ready. Don't argue and stand firm.
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!