i'm planning to use both of these models (with ml) simultaneously while recording events. Is there any difference in the footage I get? Will it be possible to swap sdhc cards with ml between these two body's?

at first I planned to buy 2x550d but then i thought i need one 600d with the flipped lcd in order to have my low ground shots done more comfortable.

I believe with the new unified Magic Lantern you can use the same cards with the one ML file on it in both cameras.