The 5DII doesn’t output clean HDMI natively. Like you said, it’ll have to run Magic Lantern software which brings in other struggles. The problem isn’t with the Odyssey it’s with the 5DII. The Odyssey is a standard HDMI port so it’ll take whatever you feed it on that connection.
Are you planning on getting an Odyssey for each camera? 3 cameras = 3 Odyssey’s? That would allow you to standardize on settings right from the get go. But if you’re going to mix formats then I’d recommend Premiere Pro as a good NLE solution since it plays any format without conversion (h.264, mxf, ProRes, DNxHD, etc.). Pluraleyes is probably the fastest way to sync everything if you don’t have a way to jam sync to timecode.
And yes, when you plug in an external monitor to a Canon DSLR you lose the onboard LCD display (at least on the 5D3 and 5D2).
Ryan Holmes
http://www.ryanholmes.me
@CutColorPost