The problem you are facing is that there are (at least) two methods of producing superscripts and subscripts.
The first method is to use actual superscript and subscript numerals defined in a particular font. Typically, such numerals are available in OpenType “Pro” fonts (i.e., fonts that have expanded character sets). In this case, the text point size doesn't change when invoking a superscript or subscript, but rather, the alternate superscript or subscript character from the font is used at that same point size. In this case, Preflight won't erroneously show you an error for superscript or subscript characters.
The second method is for fonts that don't have special superscript and subscript numeral definitions. In this particular case, the application program simply invokes numerals from the current font at a smaller point size and changes the baseline for their display. For example, a subscript numeral for a 10 point text may be 5 point. It is in this case that Preflight will show an error if you are searching for text smaller than 6 point. Acrobat and Preflight has no way of knowing that the 5 point text is being used as a subscript character. All context is lost at this point. And unfortunately, there isn't any solution to this other than using fonts with actual superscript and subscript characters as well as software (such as InDesign) that can take advantage of same.
- Dov
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