They just clamp around the 2 frame rails like the motor mount in these pics pic, but the 2-piece style mounts dont have a top plate and cost less. They just use the engine block as a structural support instead of a top plate.
Yes that would work fine, and the 6.5hp Duramax would bolt right on that motor mount.
The motor mount in your link sets the engine at a 15-degree angle. The only reason for the angle is just so the carb/air cleaner will clear the RR tire on side engine racekarts. You could use an 15-degree angled style mount on your project if you want, but if your engine will be located in the center/back of your kart, It might be better to use a motor mount that would mount the engine flat/level like the one at this ebay link: http://www.ebay.com/itm/Racing-Go-K.../190418996630?pt=Go_Karts&hash=item2c55db4d96
Here's a pic of a side engine racekart with a 15-degree motor mount, I think It might be better to use a flat motor mount in a rear engine kart.