CSV2XL.SBX 2.1(277) adds a new CSV2XL ini file option to set footnote references to subscripts:
[Format]
FootnoteSubscripts=1
When set to 1, any occurrences of "(#)" or "(##")—where # represents a digit from 0-9, e.g. "(1)" or "(13)"—in the banner or column titles will be converted to the corresponding subscripted number. Similarly, "#)" or "##)" at the start of a footnote will also be converted. The idea is to mimic the standard typographic handling of footnotes in traditional publishing. Unfortunately, the subscript font may be so small in Excel that they are to read. Consequently it it it remains an option, defaulting off.