I have always been concerned about flip cuts, but haven't things changed with new systems and machinery? I watched a video of a Thermwood router cutting the secondary side first with the flip cuts, then cutting index edges on two adjoining, then flipping the part. The operator had to register to stops, but it looks like a far better situation than by flipping cut parts and indexing each.
Few of my seeds, if any, have no-flip parts. I have captured 3/4" backs and all lock tenon joinery.
Was that a software upgrade or does one have to have a newer machine?
As long as you have very accurate index stops and accurate sheet measurements (length and width), flip operations work very well. Make sure you have both X and Y index stops and you set up your flip ops to work with these index stops.