i dont' think there is enough info on the VF-1D to make arguing about it productive.
In the end all we see is that it's a 2 seater, CAN participate in combat, and MAY be used for training dispite any direct indication that it actually IS used for any kind of training. oh and that at least one of them was painted orange and brown.
Given that stageringly small amount of info, you can pretty much think what ever you want about it with no evidence to prove you wrong.
Personally i think it was probably a live fire testing machine, maybe even an early run to test fesability of having a back seater. It's obviously fully combat ready, but maybe there are only a hand full of them since we only see what.. two?? in the whole serise?
The fact that it's bright orange makes me think it's a test/protoype/experimental plane. orange doesn't usually mean "trainer" in the military, it usually means "test"
It may even be a prerunner to the elint and ostrich (sp?) variants that came out later.
but like i said, there is next to no evidence as to what it's for and my speculation tells us more about what i want it to be than what it is.