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Unfortunately, it cannot work like you want. In the ODF specification section 20.183 fo:font-size in specification part 1 you find,

The value of this attribute is either an absolute length or a percentage as described in §7.8.4 of [XSL]. In contrast to XSL, percentage values can be used within common styles only and are based on the font height of the parent style rather than to the font height of the attributes neighborhood. Absolute font heights and relative font heights are not supported.

Important part is "are based on the font height of the parent style rather than to the font height of the attributes neighborhood". And 'parent style' is a character style in the hierarchy of character styles.

You need to build your own character style for markup in a footnote and maintain it manually. In addition, there is no way to bind a character style to a paragraph style.