Mine's a 41/09 and has the flat keyboard, which I've never had a problem with. I think the real problem here is that some people just love to complain. You've got a portrait virtual keyboard, a landscape virtual keyboard, and a landscape physical keyboard, so if you don't like one, use the other two! It's not a huge issue. I've used the physical keyboard and can type pretty fast with it without issue, but I use the portrait virtual keyboard most often because that's how I'm usually holding my phone. I prefer the landscape virtual keyboard the best (and, consequently, can produce the highest wpm with it) - it's simply a matter of preference. As for why there's a difference, if it's not simply manufacture variance, as has been suggested, I'd guess it's an aesthetic thing - the Droid itself is square and bulky, so a flatter keyboard would seem to fit that aesthetic better than a "bubbly" one, I would think.
Also, for those commenting on the flatter keyboard issues, haven't experienced any of those described (had my Droid for 2.5 months now). As for the shell/holster catching, if you're referring to the shell/holster combo that Verizon offers (the phone slides into the holster face-in to protect the screen), it catching has nothing to do with the keyboard. If you slide it closed and look where it catches, it's the point where the tab that holds the back of the shell on the back of the phone catches on the lower tab (if you have your phone held in landscape orientation) of the smaller frame that goes around the touchscreen. I've really only had that issue if I'm holding the phone with my left hand while trying to slide it closed (because my left hand pinches the shell together just a bit and that causes the tabs to catch on one another).