I had the same issue using unity/gnome on a laptop with 1-3 monitors. After I switched to i3 I was forced to set the monitor config manually with xrandr. I set up keyboard shortcuts for switching between 1-3 monitors. This fixed all the issues with automatic window placement since the window manager no longer tries to do this in an automatic fashion.

Tiling window managers definitely have a learning curve, but after I spent a weekend switching to one, I can't see myself ever wanting to go back to floating windows.