I am just starting down the road of using Mach3 and Shape3D (creates the GCode file) for shaping surfboards.

I haven't been able to find a definitive answer regarding the tool starting point options.

The Shape3D software uses the tool home position as a starting point you can choose other points but would prefer to just start at the work piece given various sizes of the work pieces.

Is there a way to do this using Mach3 or do I have to always configure the start point in Shape3D (GCode)

Work coordinates are different from Machine Coordinates and are defined under G54 (default) to G59.
Under G54, you move the cutter point to where you want the starting point to be and then set x , y and Z to zero.
Then only you start the G-code program.
You can always save the coordinates under G55-G59 so that you can recall different origins.