Have had an aluminum service body on my F550 for 15 years now without any corrosion or paint problems.
If the material, being steel or aluminum is prepared properly, you won’t have a problem either, my deck was washed down with acetone and powder coated properly, any steel deck should be sand blasted to shiny metal and primed and powder coated too. Don’t cheap out on the finish either way and you won’t have problems, steel over aluminum will make it considerably heavier even though you have a 550 it will still make a difference in the final GVW so look at all your options (trailer tongue weight, generator, extra equipment, camping gear, fuel) they all add up and the next thing you know is the 550 isn’t enough.