Just to clear this up if you are in Victoria and are not under the old power to weight P plate laws which were before july 2007 then you are unable legally to have any sort of engine modification to your car. This means even having a different type of filter IE ram flow on a 4ac infringes on this law, Red plates are in the same boat only they would be worse as they can now be specifically target as they stand out alot more then greens because there are still a heap of people on the pre july 2007 laws.
I got my p in 2008 before the red p plate laws came into effect and I know I cant have any engine modifications legally, though you could most probably pass a 4age as stock to the relevent authorities you can still get done for it.
Also just think of the insurance side of things , if you had a big accident and they found out that you had change your engine you can get into serious shit because of it as they will probably try to not pay for any damaged you do to your car or other cars depending on what happens.
As for the factory option case this is true but untill it is proven properly that toyota did bring in the mythical 41 jdm ae86's and that information is submitted to vic roads / other state road offices then we cant do much.