@7dau253mrwry4spf: You don't have full control over whether a link is interpreted as a footnote and hence gets the popup, or as a navigation link. A lot of it is based on heuristics the software uses to decide. But, basically, if the destination looks like a footnote type destination (later in the book, not to a file or heading, destination text isn't to long), it will be treated as a footnote and displayed in the popup. Otherwise it will be a navigation link. Links to headings, or without an anchor will always be navigation links.
The kepub renderer does at least partly support the epub3 footnote syntax. You can try that to force it, but, I can't remember exactly how well it works.
There has been a lot of discussion of footnote links over the years. I don't believe that anything has changed recently, so a search will find more details.
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