Were you asked whether you were VFR or IFR when you requested the initial zone transit? Did you transmit what you were when you made initial contact with them? Either way if the transmission included that snippet of information then that would have been passed on.
Having said that it is up to you to say if you cannot accept a particular type of approach - so your newly qualified in your example scenario has got to open his mouth should he be given something he cannot accept. However, it's a two way street, and to be quite honest the first ATC unit shouldn't have assumed anything - they should have asked, especially as this would have decided the manner of your initial zone crossing.
As we always say:
never 'assume' - it makes an 'ass' out of 'u' and 'me'