The bots use the Normal work handling, so most likely yes, you need to manually handle blights ;-D

Thank you for responding Haplo_X1.

Perhaps this is something that can be implemented in the future? At the very least to prioritize cutting blighted plants once the user tags them. I'm not sure if it is as simple as checking if a plant marked for cutting is blighted, is yes, then don't call the games normal work handling, and cut the plant. I am thinking during most game time there are no items flagged for cutting so the check will pass with little to no wasted cpu cycles.

I'm probably way off base. I have no idea how these mods are implemented.