Here is something from Lex at DeskProto on that setting of radius in Mach3:
About Mach3 needing the radius of the part for its speed calculation I may be able to shed some light:
The feedrate as set in the G-code is a linear feedrate (mm/sec, inch/min, etc). It is easy to calculate the speeds for X, Y and Z to achieve this prescribed feedrate, however not for A: the further away the cutter is from the rotation axis, the lower A-speed is needed. Many controllers can't do this calculation, and some controllers solve this by asking the user to enter a radius, in order to simply use that value as distance to the rotation axis.
As DeskProto uses inverse time feedrate this setting does not apply to the G-code from DeskProto.