About the automail - I know! The removal of Ed's automail felt like a random retcon for no real reason. The makeshift automail doesn't seem to especially hamper (or help or... anything) Ed in any plot significant way until he busts it crash-landing. He could as easily have had his original automail and replaced it then instead.

Although, I do think the final shot of his automail in the series proper is meant to be symbolic or something because the hand is normal. When we last saw his automail, he still had the hand he transmuted for himself in the gun factory after Wrath absorbed the original one.