Seems to have problems with SRD's SuperToolsEngine. Presumably you're defining the windows in a way it doesn't understand, as its this code:
Scene_Base.prototype.initCustomWindowPositions = function() {
if(!$dataWindows[this.constructor.name]) return;
const children = this._windowLayer.children;
if(!children) return;
for(let i = 0; i < children.length; i++) {
const win = children[i];Not that I'll need to use it in this case, but unfortunately, it's generally needed for the project to move windows and UI stuff around, so I can't be without it (the other console references are just various plugins using create/update scene).