Using lua you can do something like this;
So if for example your third party app happened to be AutoHotkey you could write an ahk script to reposition the windows and then execute it from within a lua script using something similar to the line below.
Pay attention to the use of the single quotes and double quotes surrounding the path or it might not execute.
os.execute('"C:/folder/your_file_to be_executed.ahk"')
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