Hi,
the early M6 is quite common. The machine is being set up to do the job, so the CAM program calls for the tool to be used. The fact that it may already be in the machine
and therefore no M6 is actually required is completely unknown to the CAM program, so it calls for an M6 to ensure that the right tool is used. Likewise it will call a G43
for the tool, after all the tool length offset is an important parameter, that you have arranged it so the tool offset is not required is again unknown to the CAM program.
As far as the G3 moves, use MasterCAM to simulate the toolpath, is the toolpath correct? The rule is to use the CAM program to simulate the toolpath rather than doing a dry run on the
machine. That absolutely requires that the CAM program have a perfectly accurate description of your machines motion characteristics, things like axis orientations etc.
MasterCAM has an excellent, albeit difficult to use, machine description module. It will take many hours to learn to understand the machine description module but is essential if you want to
produce sensible code without you coming along and editing it.
Craig