Aren't gracious and condescending antonyms?
Not originally. Indeed, it remains that one meaning of to condescend is to forgo rank or privilege and join people "below" you as equals.
This was so often used ironically, of someone acting as if they were talking to an inferior, that it became the predominant sense.
Vouchsafe underwent the same partial change, and can mean either bestowing something from a superior position (which would be a graceful act), or else as if from a superior position. So it can be used both to match the old sense of condescend, or the new.
The really confusing sense, is that sometimes people talk of "vouchsafing prayers to God", which matches neither sense. My guess is that it's a matter of people only knowing vouchsafe from religious contexts (God is often vouchsafing, or being asked to vouchsafe something, in religious writing) understanding that it means "give", but not understanding the implied imbalance of the transaction.
Edit: Or another possibility is it was originally from asking saints to vouchsafe to intercede with God, on the matter of the prayer, among those denominations that believe in intercession of saints. Still no more than a guess.