Navigate first to the win32 folder within the Starbound folder. In my case it's at C:\Program Files (x86)\Steam\steamapps\common\Starbound\win32. Since this is where the asset_unpacker.exe is located by default, the .bat will refer to this one without the location of the unpacker needing to be specified. Create a new text file here and enter this (make sure you edit this to fit your directories):


Replace all of the parenthesized text (except the (x86) of course if that is in your directory) with text that is relevant to the mod you are unpacking!
To find the directory of a mod, click the gear in the bottom left of Starbound's main menu and click on a mod to see its details. Navigate to this location and copy the directory entirely to use in the text above.
Example: C:\Program Files (x86)\Steam\steamapps\workshop\content\211820\729426722\contents.pak

Save this text file as a .bat when you are done.

Double click on your newly created .bat and the mod should now work and be read by your server! Servers started by the starbound_server.exe in the win64 folder read from the mods folder by default, so the unpacked mods should instantly be in the right place.

If you wish to make your .bat unpack multiple mods at once, copy the entire code, hit enter at the very end of the first line, and paste it onto the next line. Change the directory to that of your next mod, and change the name of the folder that will be created.