Well, it seems important to me. For doing non-12-TET tuning, and for pipe access, these can be important.
None of that is practically supported by any tool out there, though. Besides, I'm not sure if this sample re-use thing can be guaranteed to work with each and every tracker/player - I do remember that DUMB has (had?) this concept of only ever reading files sequentially and never jumping backwards, which could pose a problem with such samples of course. I have no idea if this limitation still holds, though. But even then, it's still not a practical problem for tracker users because as said, no tracker software practically does this. It's strictly a developer problem, not a user problem, and this thread so far was only about people talking about their tracker of choice as a user.
And the PDF lacks a table of contents page.
It does have a TOC which can be viewed by any proper PDF viewer (usually in a treeview next to the page display). But that doesn't really matter since the latest versions use a CHM file for the manual instead of a PDF.
it doesn't even have SQL
"Even"?! Are you aware that no tracker out there has this feature, and that you are pretty much the only person that ever came up with it?
But please, go ahead, take any tracker, add an SQL interface to it and demonstrate how much easier it is to edit modules by writing SQL statements rather than by typing in notes and using a GUI.