The automake manual already mentions this, I actually looked in the automake manual first. And the reference I got to first (don't know why) is the one in the `Program variables' node, which says "Some variables are inherited from Autoconf". So I went to the Autoconf manual instead of looking further in automake. Perhaps an @xref{User Variables}? Perhaps not.
but yes, I agree that adding another sentence in the autoconf manual can't hurt. Thanks.