Yeah, the rear dish is non-standard; it’s built offset to increase tire clearance without the need for longer or dropped chainstays. But that also means you can’t just take any rear wheel and put it on the bike—you have to take it a shop and have them adjust the dish. Then you won’t be able to use that wheel on other bikes. As far as I know you can’t buy stock wheels with this dishing, either. It has to be done after the fact (unless you do a custom build, of course, in which case they’ll build it with the appropriate dish).
Otherwise, the only other real “issue” is the proprietary crankset removal tool for Cdales. Not a huge deal imo, but it could be a problem if you want to remove the crankset yourself or take it to a non-Cannondale shop.