Jason,
Not sure how the newer machines run, but the older Biesse machines would park the head on the side of the table the part was being run on. Thus when the part in the right zone was complete the head parked in the back right side. When a part finished in the left zone, the head parked in the back left. If while running a part, the head crossed the center line and the operator was on the mat, the machine would stop, until the operator stepped off the mat and pushed the button to continue.
The way the machine was set up, we are able to pendulum process the maximum part for each zone.
What is the setup for the pods on the new machine you are looking at. Is this automated or manual. Either way there is setup time between parts, you should take in consideration. Also, pods will be hit and need replacing at a cost.
We used our Biesse similar to what you are thinking. Cut the parts on a beam saw and then run parts on the Biesse CNC. We have a flat table machine so there was no set up tip between parts. Though, I see you would be horizontal boring with your new machine which is something we do not do.
Since we have changed to a new flat table router and do mostly nesting. If I were to go back to cutting parts on a saw and machining, I would lean toward a vertical cnc or a flat table machine and a dedicated machine to horizontal bore. Horizontal boring is a time consuming process on a CNC and is much more efficient and accurate on a dedicated horizontal boring machine.