You have your job & then you have the role that you specialize in, for example, I have ENG in my name but I'm only a normal WP Trooper. This means that I can undergo engineering inside the ER when needed. Before I became a part of WP I had MED in my name so I had medic as my specialization but I was an ARC Trooper, this meant that I was allowed to be in the medical bay & undergo normal checkups or help under any emergency in the medical bay.
How it works for Pilot I don't know but I believe that it's almost the same, you are for example an ARC & have PLT in your name then you should be able to do pilot stuff (fly etc) but as I said, I am not sure.
And from what I know of you can only specialize in 1 role, doesn't matter if you are medic trained or not. If you choose at that moment to specialize in Pilot or Engineering then you can not do medical procedures inside the medical bay.