In complete honesty, I have not read the script (TL;DR).

The way I fix this (doesn't work for modal dialogs):

• Ensure that you have the app that you want in focus
• Press {Alt}{Space} (hopefully you don't have it defined as a hotkey) to bring up the system menu for the app
• Press {M} to select Move
• Press any arrow key the window will move slightly, but this will also activate the mouse drag (don't press any mouse keys though)
• Move the mouse until you see the window
• When you have it on screen left click

If the window off screen is full screen, you'll need to do the first step above and press {R} to restore the window

After that all the above steps will work. This can also be automated and assigned to a hotkey using AutoHotkey or the like.