I'd love to use more than one window, but they're completely unpredictable and really hard to configure the way you want. Magit buffers will open in one way, Cider Error buffers open in some other way. And the behavior will also change based on your frame size... You can sometimes configure them, but only from the limited behaviors provided by the package itself. The behaviors are different in different packages and there is no configuration/coordination in the "runtime"

There is a central configuration, see here https://news.ycombinator.com/item?id=43642743