This was not a Catholic clergyman's source, that's C. Schmidt, Schaff-hersog saying it.
Well, then the problem is simply that YOU aren't reading the text carefully enough. In the portion you quote, Schmidt clearly indicates that the Manichaeans were a separate group. In fact, the only groups he lumps together are the "Cathari, the Bogomils, Patoreni, Albigenses..." which he says were "all of the same family." What that means is that he is not lumping them together with the Manichaeans - he says NOTHING about the Manichaeans being "of the same family" as the rest of these. That delusion is entirely of your own making, coming from an imprecise reading of the actual text.
In fact, when we consider the timeline involved, it's clear why Schmidt chose to word it the way he did.
The Manichaeans who came flowing west did so in the 2nd-4th centuries, several centuries before the Paulicians, Bogomils, etc. In fact, if you will recall, none other than Augustine was originally a Manichaean. As has been noted, even after his conversion to Christianity, he retained a lot of his Manichaean mindset. Given the influence which Augustine has had on Roman Catholic doctrine, it's more accurate to say that Catholics are Manichaeans than it is to say that the Bogomils were.
My bad, that should read "3RD-4th centuries"