The answer according to HaGaon Rebbi Abba ztz"l [my email box has been so overflowing with terutzim I can't handle all of the volume of mail - see hashtag my-mer at bottom]:
Rav Yehudai Gaon was 100 percent correct!! We CAN compare טומאה and איסור לבעלה. The fact that she is a niddah is the root cause for both her טומאה and her איסור לבעלה. So if we learn that she must go to mikva for Taharos that would mean that she also has to go to mikva for her husband.
But I hear you saying - so explain Tosfos, who make a distinction between the two!?:-)! [If you weren't saying that then I am hearing voices which is another issue].
The answer is that when it comes to ספק טומאה ברשות היחיד, even though with respect to טומאה it has a din of being definitely טמא even if there is a ספק ספיקא, nevertheless the ספק ספיקא of whether she is a חפצא of נדה or not has not been clarified and remains a ספק ספיקא. Therefore with respect to her איסור לבעלה, we stay with our ספק ספיקא and she is permitted. [And also regarding ספק טומאה ברשות הרבים which is טהור מספק where the ספק has not been clarified, when it comes to איסור לבעלה she will be forbidden since there is but one ספק].
So the distinction is between where she is a ודאי חפצא דנדה in which case we can derive classify טומאה and איסור לבעלה together. And cases where she is a ספק חפצא דנדה where her איסור לבעלה depends on the number of ספקות involved - 1 or 2 while her טומאה would depend on the רשות. [Does saying "חפצא דנדה" count as "objectifying" women? :-)].