A user has come up with a way to get rid of the popping windows caused when using Lua on Windows. The link here is to the issue, Prevent terminal windows from popping up during start on Windows · Issue #17193 · darktable-org/darktable · GitHub.
For those who don’t want to read it, it consists of creating a shortcut with the following as the command
C:\Windows\System32\cmd.exe /S /C "start /B "DarkTable CMD" "C:\Program Files\darktable\bin\darktable.exe" > "C:\Users\jeanr\Documents\Darktable\log.txt" 2>&1"
You need to change jeanr to your username. After you create the shortcut, you can go to properties and change the icon to darktable.
What this does is open 1 window and then start darktable. darktable then uses the already open window to access the operating system, therefore no popping windows.