Footnote references to Appedix

This is a dedicated feature doing precisely what is intended to do, rather than a temporary fix to get around a bug; it is not a workaround.

That aside, yes, I would not strongly advocate for using Scrivener vanilla for the forms of writing that require more infrastructure like this. Scrivener is much better when it is combined with a writing method designed for this kind of work, and it has extensive built-in support for integrating with Markdown. You will have far greater flexibility, more professional file formats to convert to, better quality documents, and it is an easier typing convention to work with than Scrivener’s in my opinion. I would only find the latter suitable for a few cross-references here or there.

With Markdown, you simply type in Refer to [Binder Title] like that, and that can often be all you need. You can of course type brackets wherever you want, in any software, or any area of the software (such as footnotes); you don’t need special technology. But furthermore, this format makes it very clear what you are referring to, as a writer, you don’t have to hover over a link and wait for a tooltip to see the target. That is how I type in the many hundreds of cross-references in our user manual PDF. The post-processing I use (LaTeX), handles the nomenclature and all the numbering for me, and Markdown handles the formatting of putting it into parentheses when the reference is given as an aside. It is also capable of targeting tables and figures directly, which is something Scrivener cannot do.

Better cross-referencing is only one small benefit of using this more powerful side of Scrivener though. If you are already familiar with Markdown, have a look at Chapter 21 in the user manual. This mainly covers where Scrivener goes beyond your typical Markdown editor though, for the basic rudiments of how it works with it, this post is a good starter, along with the post it links to toward the top.

And again, I left it implied, but the user manual PDF is written in Scrivener using Markdown. So that is a showcase of some of what this approach is capable of.