The thinking is there's a separate partition for the desktop OS. IF the bootloader is unlocked, rom developer may be able to liberate that extra 512. But the Bionic won't be out until Apr/May and I suspect we'll see something a bit better, something with 1gig, not long after that.
The main difference, aside from the docking app (which may or may not interest you, I think it's still a bit of a novelty) is the Bionic is LTE which will have fantastic speeds, but it also will be capped (goodbye unlimited data) and possibly $5-$10 a month more than the $30 for 3G.
The other thing - and I don't know that this will change any time soon - is while Bionic has HDMI out I don't think it can't mirror video, mostly just for photos. The Atrix seems like it should be able to run video off your SD through the docking app, but don't quote me on that.
I doubt you'll have a decision to make before LTE pricing becomes available. Might be too tough to call right now without knowing caps and pricing. But I wouldn't attach any weight to hopes that extra 512 on the Atrix can somehow be liberated. Heck, you don't even know what kind of developer support it will get and eventhough the installed base for both phone is currently 0, there are a lot of D1 folks who will probably upgrade to the Bionic and there's a much larger Android base on VZW (so probably outsells the Atrix and gets better developer support as a result).