For Cut2D I just drawn the overcuts in CAD as my version of Cut2D doesn't automatically do this operation.

But Cambam has an option to overcut the internal corners to allow something with square corners to fit inside, but you will have gaps on the outside as Neale mentions.

Scroll halfway down:
http://www.cambam.info/doc/plus/WhatsNew.htm

Or if I need dead square corners in wood I just file them square by hand - you could do the same in carbon fibre?

I know this is off topic slightly but on metal you can broach square holes, you can spark erode square holes (or whatever shape you machine the eroder bit to be), and if you have a look at John on NYCCNC you will see machined square holes being made using a special broaching device:

(scroll to 11:30 for the machining operation)
https://www.youtube.com/watch?v=-MidOdzxT7k