Unless you want it to “look” like an Arduino shield, I would not use the outiside dimensions of the Arduino. The Fab house may well charge you for the extra square inches of board space.
The only reason I’d use this footprint would be to get the spacing of the headers correct. Then I’d make the board as small as possible to complete the circuit I wanted on it.
Note: I don’t know that I have the pin headers on the proper side of the board in the 3D view. I also have some SMD parts on the back side of the board; which I did check for clearance of the MC on the Arduino Uno board.
With all the SMD devices, with a fairly simple circuit design, I decided to just have the board fabbed instead of soldering the parts to breadboard modules and breadboarding the entire circuit. Breadboard connections can sometimes be flakey for many different reasons.
In the end, I’m pleased with doing it this way. I used OSH Park for fab, I have no connection with them other then as a satisfied customer, and I got the board back in a reasonable amount of time for fairly cheap. I will be doing other small SMD circuits this way again in the future.