True, but with the unique end delimiter, you can add an interim step to fix that: find any white space followed by the unique character and replace it with the reverse. Try something like this (I'm on a system without Word right now so can't test it);
Find what: ([ ]{1,3})(ÿ)
Replace with: \2\1
Wildcards on
This would handle the case of 1-3 spaces. You can adjust if there are >3, and could add codes for tabs and fixed spaces if applicable. This method will only "fix" the ending spaces; internal spaces will still remain superscript.
Your point is a good one BTW: in a "normal" manuscript that uses the Footnote Reference character style, the superscript won't include the trailing space, but when the superscripting is done manually, the trailing space erroneously retains the formatting. I often see instances like 1iere where the superscript "iere" is squished against the following word. This particular fix is included in a routine macro I use to tidy up manuscripts coming in.