This will definitely save the constant remuxing to format that Premiere/ Media encoder supports
You can just write a cmd command to do that, and it's very easy:
@ for %%1 in (D:\outputFolder\*.mp4) do (ffmpeg -i "%%3" -c:v copy -i "%%~n1.aac" -c:a copy "Muxed_%%1.mp4")
You can even add a line to delete original files once they are done, and that's after 'pause', which you can confirm it before let it deletes.
Don't let Vouk do all the work, would you