I downloaded CNCWraper and tried some simple text on a bar of aluminum but it wants to put the 0 position in the middle of the part.
Not just the center of the A axis but in the center of the X axis as well?
This is not something that CNCWrapper is doing. It is the result of where you set your origins in the CAM that produced the original toolpath.
CNCWrapper when converting code, or "wrapping" it, does only two things.
First it changes the designated axis definition. Example, I set it to change X to A.
Second it scales all the positions for that axis to read in angle rather than linear units. It arrives at this scale value using the diameter/radius value that you enter. This is the ONLY thing the diameter/radius setting is used for, to establish the scale factor.
The important thing relating to your query, is that CNCWrapper DOES NOT alter the Z axis position values.
In the CNCWrapper help files it does recommend using the centre of rotation as the Z axis zero. And for most jobs I agree with this recommendation.
However if you choose to use the surface of your existing cylinder as Z axis zero, that is fine.
So as far as wrapping with CNCWrapper is concerned, where the origins are set is something to be established in your CAM program.
HTH
Greg