Do you mean the scio quod?
Yes. In classical Latin, you'd usually expect an accusative-and-infinitive clause instead. However, I think I see where Castellio was coming from because:
1)
Pario seems an obvious verb to translate classically whatever was translated as
operatur in the Vulgate. It was my first idea as well.
2) Now, of course, if you use an acc.-inf. clause in a literal translation (keeping the active voice), you get something ambiguous, with the two accusatives, which classical authors would surely have avoided.
3) What you usually do in those cases is to turn the construction into the passive, but the passive infinitive
pari sounds rather unusual (I don't even know if it's attested at all).
Therefore, whereas I decided to use a different verb entirely, Castellio must have decided to go for something of a stretch to keep all the subjects nominative, while avoiding the slight change in meaning or perspective that I used (namely "X is born from Y" instead of "Y gives rise to X").
Illud scientes quod... = "knowing (that, namely) the fact that..." Unusual in classical Latin, but maybe not entirely impossible.