A hypothesis of evolution was in existence in the early 19th century (Lamark) along with a linnaean system of taxonomy. I find it unlikely that Jefferson wasn't aware of the concept of evolution and species identification as books on these subjects were in his library.
Moreover, Jefferson was aware of the large fossils of unknown species in Kentucky (Big Bone Lick) and even traveled there to personally observe them.
One of the things he specifically told Lewis to look for species that were similar to those fossils (none were found).
Consequently, Jefferson's concept of a 'creator' was much broader than the biblical one.
BTW scientific theories aren't 'invented', they're discovered. Machines are invented.