They were, but the Python III, as per images.
The EM/FM upgraded F-5's all left embraer with the new green-gray camouflage, even the prototypes.
And here's another:
Please note the F-5E written in the tail, as opposed to F-5EM.
Also, picture is from CRUZEX 2002 exercize, roughly three years before the first modernized F-5's were received.