I think that the key here is how much power can the stepper drivers produce? The Farmduino uses the same, or similar, driver chips to many 3d printers, which all have a similar small stepper motor size. Although your proposed upgrade uses far more powerful stepper motors, this power has to be delivered by the stepper motor driver board, which is designed for the small stepper size on the Farmbot.
Upgrading the motors to a more powerful variety would only work if the drivers are able to provide the extra power that larger motors need.
If I was considering this, I would find out how much power the drivers on the Farmduino can produce and start from there.
I should have read your post properly - sorry I didn’t notice the link you provided. As long as you pick up the Step, Dir and Ena signals from the existing driver sockets, this should be fine. I’ll be interested to hear how it goes if you proceed, whilst the existing steppers and drivers will work well if everything is mechanically right, there isn’t a lot of room for errors creeping into the mechanics. Stronger steppers will provide a larger “brute force” approach to issues such as misaligned rails, or debris getting mixed up with the mechanism.