This has been included in the latest (2024) version of Flare – by default, PDFs now have numbers appearing in the index using natural ordering.
From the list of
customer reported bugs that have been fixed in this release: "183194 - Index Entries Sorted with Classical Alphanumerical Order for PDF Output, Index".
What I can't see is whether there's a way to select alphanumeric ordering if that's your preference.