Let me start by saying any advice I have is from personal experience on personal motos. I don't work as a bike mechanic I just work in similar fields. Any tuning I do is with my butt dyno, dig? That said I do like to fiddle with my stuff to get it right and do have a BSME with almost twenty years working on stuff so I'm invested. Also I raced two strokes for a bit and you can't do that reasonably without being able to jet a little (PWK and PWM Keihin carbs). Never could ride that bike as fast as I could make it go. So I'm an overeducated bookworm mechanical hack motorcycle enthusiast. Take what you want and leave the rest...
In your case my experience is saying you want that choke. On the downdraft CR's installed on the M900 (or any 902cc desmodue for that matter) they are finecky on cold days. I can't even imagine if I had to kick the thing. Even with one cylinder. Half the time it would be a total chore. It takes a refined routine of throttle twists, magic button, and sometimes a little babying of the throttle plus a warmup period. I'd have to say 20-40% of the time I have to hit the magic button twice. Without that button life would suck.
On the DRZ with the FCR-MX it's another story. Pull out the choke button starts right up. It has a magic button as well but the success rate is better. Also the thumper is easier to stumble out to a halt when cold. So since I have a choke on that one I'm going to assume that's the ticket.
From an exterior standpoint they are certainly different. Outside of the aforementioned choke the AP is different and less exposed and the float chamber is bigger. Also, as pointed out by another internet source, the needle for the MX has seven positions and for the standard CR there are five. More adjustability must expect us to be changing altitudes (or something) more.
Here are the major differences as listed by Sudco:
http://www.sudco.com/keihin.html
I'm assuming those features listed are some pretty desirable stuff on a dirtbike I wouldn't care about on a street bike (CR style).
More stuff on FCR's see post #2 here:
http://www.atvriders.com/vbb/showthread.php?367038-School-me-on-FCR-carbs
The FCR-MX 39 on my DRZ came with it installed by PO (horribly jetted of course) and only has a choke. I think ALL the MX series come with a choke. I promptly threw on an aftermarket full system to ensure I maximized my practical experience in getting it jetted properly. If I had to do it over again and bought the one I wanted I would have gone the next step up. Not for the air cut valve the bike shouldn't afterburn if jetted right (only if you need to make emissions guidelines should that happen) but for the hot start. Crashing, falling and the subsequent flooding makes restart a bitch. That hot start valve on the next model sounds like a great idea. Next model up from that includes TPS and ..... who cares? If the ignition system doesn't need it forget about it. I'm not racing it. So the current one I have is order #016-925 but I would have preferred the #016-926 (reading from Sudco page here). I'll try not to crash too much and it won't be an issue.
So then you say why bother with the standard FCR on the inline 4's, big twins and other road machines? Simple: they all have magic buttons and stay on the pavement. Made to go fast around tracks and stuff. More purpose built and less all purpose. The difference is subtle yet pervasive.
All this of course IMHO. Thanks for asking you made me look and I always pick something up when I do that.
My next carburetor adventure is with a handful of Mikuni TM33 pumpers and DR350's. Sadly Keihin does not make a fit for that application. The jet collection continues!