Thanks again Mon2, that's massively helpful!
I've just had a quick play with cad2cad and while old and clunky, I've managed to very quickly get some results with it. From what I can tell thus far it seems like it will quite easily process the data and spit out a nice VIOS text file. This is all we need - further processing and optimisation can be done on the machines themselves.
I've compared VIOS txt outputs from the two tools and they are very similar: the primary differences is that cad2cad is translating to the machine board zero (5mm in from the bottom right corner) and it has the nice visual representation of the component locations and orientations. It's also easy to specify the circuit fiducials in cad2cad. I believe the zero translation doesn't really matter, as the board offset just gets set to suit on the machine.
You're planning to buy a new Assembleon machine? Do they still support this old VIOS format? Is cad2cad still the tool they recommend people use?!
Yes, I have actually spoken with Andrew, the author of PCBSynergy. I was able to get Altium files to work but there were issues with the coordinate system origin, so it's easier to simply use the pick and place CSV file that Altium can generate.