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I came to report the same issue. Here's another example of the formatting issue for the footnotes when printed within a loop: https://rpubs.com/ddsjoberg/688904
With the latest version of gt, this doesn't work at all. I don't think we'll support this usage because fixing it will probably increase the risk of other problems.
In the example below, the same GT table displays the footnote differently when inside and outside of a loop.
title: "Report"
output:
html_document: default
\
\
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