The question of whether the mutations occurred by a "an unguided, unplanned process of random variation and natural selection", or whether there is an "Intelligent Designer" manipulating these mutations would, as I see it be another question entirely, and frankly, I can't see why science would have any position on that.
I guess you are trying to define a difference between Darwin and modern evolutionary theory, based on Darwin's inability (or disinterest) to discuss possible sources of mutation?
There's not much debate now that as far as evolutionary theory goes, all we have evidence for is genetic mutations as a source for most physical mutations, and that genetic mutations occur randomly as a natural part of the reproductive process.
There could of course be a guiding "hand" in the mutation process that is as yet undiscovered (intelligent or otherwise), and it could be that there is one that will always remain invisible. Science will not address it as long as it remains "invisible."
The problem here is that the cardinal in question is not just supporting theistic evolution, but using terminology from and indeed has now been identified as working for the Discovery Institute, which involves Intelligent Design theory. That is more than simply theistic evolution as it in part argues that there is scientific evidence for a guiding intelligence in the mutation process.
That would be the church moving into science to make claims regarding scientific findings, and false ones at that.
holmes
"...what a fool believes he sees, no wise man has the power to reason away.."(D. Bros)