I would try to clean the aluminum up but not patch it - it is functioning as a big heat sink and patching with a different material will probably not improve matters. Having a clean surface and good thermal transfer is important. I would probably use thermal mastic not the anti-oxidant, but you do need to use something applied to clean and bright aluminum. I would use a 3M/scotchbrite surface conditioning disc (or similar from Home Depot, etc) for surface preparation.