Sway isn’t intentionally trying to break your other DEs, it’s just not really designed to be used the way you are using it. Sway needs a very specific configuration to work correctly, with environment variables and other settings, and a lot of that stuff is set up differently than how it is done in KDE or XFCE or whatever. It is meant to be a standalone system, not something to layer with other DEs.
It sounds like Sway is just not what you want–I would recommend not using it. 
i3 will work much better for your use case, and is very similar feature-wise. It also takes better to layering with other DEs, such as described here.