It would be a design error to not include deleted content, as that content is contained in the section you are copying, only not currently shown due to your Track Changes settings. This fact is also consistent with the warning you get when you delete a selection that contains hidden content. In any case, it looks like at least some scripting would be required for your workflow. At least having a script that automatically accepts all tracked changes (which removes the deleted content) and then saves the file, possibly with another name, then copy the required text and paste it elsewhere. But it looks like scripting the text comparison inside FM would be much more efficient than using Excel as part of the workflow. In that case, it is easy enough to get just the visible text (that is just a couple of lines of ExtendScript code). ExtendScript supports regular expressions (at least to a certain level) so you would have the entire workflow running inside FM.
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