Hi Tim
Their only concern about you would be whether or not you would be eligible for Australia's Disability Pension because of your condition in the event that you were to decide to jack in your current job. However, if you are currently deemed to be fit enough to be in the armed forces, you would have a heckuva job to convince the MOC that you are too sick to work, chum!
The same doctors who provide the Medical Officer of the Commonwealth service to DIMA also provide a similar service for Centrelink, which is where people have to start if they want to try to claim Benefits of any kind.
If you are willing to pay £50 or so for a private, informal consultation there is no reason why you cannot make a special appointment to consult a Panel Doctor at this stage, just to get his opinion about whether he thinks the ileostomy would raise any doubts in the MOC's mind. I assume that the PD would have to tick Box B on Form 26, meaning that he has discovered "significant findings" or whatever it says. The Panel Doctors have no say in the decision-making - the MOC alone advises DIMA. However, I reckon that an experienced Panel Doctor would be able to make a pretty accurate prediction.
For what it is worth, it doesn't sound to me as if you are likely to have anything serious to worry about. The MOC would defo want to see the specialists' reports from the time and might ask you to arrange an up-to-date report before making a final decision on your meds, but they often do this solely as a precaution in case the Panel Doctor has failed to spot something important.
Please see here:
http://www.uk.embassy.gov.au/lhlh/Vi...Migration.html
Cheers
Gill