https://en.wikisource.org/w/index.php?title=Index:On_an_Evolutionist_Theory_of_Axioms.djvu&action=edit has {{index transcluded|transcluded=yes}} in the "Table of Contents" text area. Is this relevant?

In T159095#3056825, @MZMcBride wrote:

https://en.wikisource.org/w/index.php?title=Index:On_an_Evolutionist_Theory_of_Axioms.djvu&action=edit has {{index transcluded|transcluded=yes}} in the "Table of Contents" text area. Is this relevant?

That just shows that we have run a manual check and recorded that the work is completely transcluded, ie. used your tool to check. No template or "transcluded=no" means that a check needs to be done, or has been done and transclusion is not complete. [Noting that recently that check will have produced faulty data, and I will await when we had the issue identified to a date to work out what needs to be rechecked.]

Yes, I have added these transclusions in early January to resolve task T114318. Using template dependencies is imho the right way to go because as the Index pages displays the proofreading quality of each page it transcludes some data from it. The other way to go would be to implement an other dependency tracking system and I am not sure that it's something we want to do (see how much time it took to have arbitrary Wikidata entity access with much more human power and a much more important need).

So I believe that in the current state one of T114318 or this one is a WONTFIX.

okay, we probably look to update documentation so that people know that whenever an index page is created that this transcludes the page, and this is what will show in the system, and that it is independent of whether the file exists or not.

I will ask MZMcBride very nicely if he is able to make changes to the checker tool so that the (default) check is only the main ns of the wiki with regard to the classifying and grouping of the transclusions.

I replied here: https://meta.wikimedia.org/w/index.php?title=User_talk:MZMcBride&diff=16380939&oldid=16376682.