I am delighted to share this with everyone that the improved IA-Upload tool is now available for use. The tool now provides a drop-down feature to select whether to directly upload PDFs from IA to Commons or to upload DJVUs using the existing workflow.
The tool also checks (using iwbacklinks) whether the requested IA item has already been uploaded under a different name, and if so it shows an error.
The improvements were made by User:Lautgesetz from Panlex as a part of the following Project Grant: Grants:Project/PanLex/Balinese palm-leaf transcription platform on Wikisource
There are a few more improvements to the tool than what I mentioned above and you can read more about them here: https://github.com/wikisource/ia-upload/pull/42