Re:
Right. The lowers of Rockshox aren't strictly 'magnesium', they are an alloy with a high magnesium content. They will have been heat treated after they were cast, and have been slowly hardening further over the last 20 odd years. Powder coating exposes them to 200c for typically less than an an hour, so that won't make any noticeable difference to the strength.
Powder coating.
You want to get them clean. Really clean. Sand blasting will get them fairly clean, but it can leave a grainy surface on alu. Aqua blasting is a better bet, it's a finer finish, and is much kinder to alu surfaces.
Then mask the internal bores, pay special attention to the areas where the oil seals fit.
Then have them done. If they explode, they explode. You'll be annoyed, but not as much as the operator who will have spatter all over the nice expensive wheels he's got in the oven at the same time.
And remember, they're only Indy XCs, so not then end of the world if it all goes wrong.