The controller would be a Dynomotion KFlop, so I have lots of flexibility in programming.
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I still need to run through a list of inputs/outputs for this machine, as if I allow for how I ultimately want to upgrade this machine to, then I may only have one encoder input spare, unless I move some of the differential inputs to other inputs (I've got a Kanalog, so the differential encoder inputs can be used as standard differential inputs).
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I've had a reply from the man behind Dynomotion, and he said either way would work fine, and if noise was an issue with a pot, just fit a bigger capacitor over the input wires, as you don't need that fast a response.
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If I was to use pots, then I could have an option for it to either go straight to the pot setting, or not to move until the pot is returned to near zero.
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Sometimes lots of options isn't good!
I've got a few other more pressing issues to deal with, so I've got plenty time to think about this.