My take on the theory of 49; (Since everyone seems to be doing it.)
I don't know if anyone here has read Micheal Chrichton's book "Timeline", but the story is that a group of collage kids are sent back to the 1440's to save their collage professors. But that's not relevant. Though, what is, is the theory that when one person does one thing, say, for example, you pick your arm up, an alternate world is created where you didn't, or another where you spontainously exploded. Thus, a world exists where it is still September, 1914, exactly the same as it was.
So, my theory is that the gate is a passage to a certain time, case in point, 1914 (The book as I said, was the 1400's), where all possibilities are. The two parralers, of course, are Amestris (Hagaren world), and our, the viewers world, England. So, the two times are happing synomunisly, just two with very different results from one choice, say, the invention of alchemy, in A-Universe, hundreds, or thousands of years ago. So, the gate, brings a person to E-Universe, and inversly, going from the gate there, allows you to go to A-Universe. So, when Hohienhemm was brought into the gate, and since it's the same time, he's body still existed. But, Ed, since it was a land with little or no Alchemy, didn't loose his arm and leg. And, I'm sure they gave him a shorter hair cut so you can tell the difference.
So, that's my theory. And the screaming at the end sounds like Gluttony for some reason.