No, I'm afraid it definitely is referring to the vaginal opening.
Many, many years ago, I was the Welfare Officer for the Sussex Uni LGBT society (there was no Q in those days). I had to go on a training course which taught me all of these weird and wonderful terms- 'bonus hole' was around even then (circa 2010).
'Bonus hole' is used by 'gay transmen' (i.e. straight women who identify as male) because the 'main hole' (my term, for clarity) is the anus, since men have this, too. The vaginal opening is the 'bonus hole', i.e. an extra hole only possessed by transmen as opposed to biological men.
Imagine prudish, 20-year-old me learning all this when all I wanted to do was help gay uni students feel more accepted by encouraging them to come to film nights!