Not sure what you mean by held against you. Certainly they would probably look more favourably upon someone with an open mind than one who was for example, rotary or bust. Bear in mind that the way that the system is geared, everyone starts as a potential FJ mate and are only diverted from that on the basis of aptitude. Regardless of whether you consider this to be fair or appropriate, it is the system that you would be trained under and they are less likely to select you if you are already rebelling against it. Just go and say that while you are keen to fly FJ you would be very happy were you to go the ME or RW route. Once you are in training there is nothing to stop you from expressing a non-FJ preference, just be aware that they may still send you FJ regardless.