Law Above Reason

The Gemorah in Niddah 31b explains why millah is done on the eighth day and not earlier so that everyone shouldn't be happy but the parents be sad.  Rashi explains that it takes seven days for the mother to become tahor.  The Torah Temimah points out that this reason wouldn't help for our times where we don't assume the mother is tahor after seven days.  He says this is the source of the Gra that every times the Rabbis enact a law there is a hidden reason besides the reason that is given.  I don't understand what he is saying, of course Torah law applies even when the reason of the mitzvah doesn't apply because the reason doesn't limit the din, אין דורשין טעמא דקרא, we understand God's wisdom is infinite.  However, one can't extrapolate that the same thing applies to a Rabbinic enactment.  How does he know to extend it to Rabbinic law?  And where does it say this is the source of the Gra, I know the Gra holds of this principle in regard to גלוי, but where does it say this was his source?