Same thing for me. Except that I don't feel comfortable disabling everything that needs to be disabled for Yabai to work. My solution was to use AltTab[1] (switch windows, not apps) and not use the fullscreen options. I keep windows sizes maxed, I don't have the Dock visible. I just need to alt + tab to quickly switch windows.

[1] https://github.com/lwouis/alt-tab-macos