Just remember, waterjet, like plasma and oxy-fuel cutting all have a tendency to leave a cut that is not truly perpendicular to the surface. On a long straight cut, with both ends in the air (off the end of the material) it's not generally a factor, but cutting inside corners, you will see the compensation the control makes for this. It's not too different from an end mill. When a corner is approached, the feed decels and allows the cut at the "bottom" of the material to "catch up" with the top. The bottom always lags behind. End mills bend, these other methods.....well....I won't get into all the technical reasons, but it does. Anyway, the best you can get is a little bit of a conical effect on inside corners. Sometimes it's not much on thinner material, but the thicker it is, the more the effect can be seen.
I'm guessing that either you know that and are leaving stock for machining, or designing around the WJ cuts to avoid needing a high precision surface on the edges. There will automatically be a radius in the corners, so unless the jet diameter isn't large enough, let it rip!