I think you should be able to use an ordinary paint stripper. I don't believe that a paint stripper meant for an alkyd binder would harm a powder coating because they're completely different animals. An alkyd resin has to be exposed to oxygen in the air in order to cure, and it cures by O2 molecules crosslinking the resins together. A powder coating is melted onto the aluminum at high temperatures.
But, you can't remove an oil based binder with these "citrus based" paint strippers; you need a methylene chloride based paint stripper like Polystrippa. I'd put some Polystrippa on your aluminum decking in an inconspicuous spot and check to see if does any harm.
Better yet. Pop into the place that installed your aluminum decking and get a spare piece of the stuff and see if methylene chloride paint stripper will harm the powder coating on the scrap piece.
An exterior wood stain is exactly the same as an interior wood stain except that it has some binder in it, which is what forms the solid film in oil based paints. When you apply an exterior stain, the thinner in the stain penetrates into the wood, and the dye that's dissolved in it goes along for the ride. As the thinner evaporates, the dye remains behind inside the wood, and the binder remains on the surface where it forms a film. Almost certainly, the dye will not penetrate either the powder coating nor the aluminum. So, to remove the stain, you merely need to remove the oil based binder, and that's exactly what paint strippers are intended to do; dissolve an alkyd binder film.
Citrus based strippers will soften latex paints, but they're an effective waste of time and money on oil based paints. Any paint stripper that lists "methylene chloride" as one of the first few ingredients in it (cuz they're listed in order of content percentage), will take the oil based binder off. But, still test in an inconspicuous spot or on a piece of scrap powder coated aluminum first, tho.
