Compromise.
Or just make a water table so you don't have to worry about dust :-)
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If you do go for ballscrews, then you are going to have to ensure they're well protected, whereas R&P doesn't have to be. Yes you'll get backlash using R&P, but you need to remember that Plasma is not that accurate a method, so even 0.5mm of play isn't going to have much effect on most items.
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Personally, I'd be designing the table so it sits above the side rails, that way the only thing in the way during loading would be the gantry. You then only have to handle dust from above, instead of spray back/dust coming up the way as well. You will still get some dust coming up the way, but hopefully a lot less.
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Have you had a look at the swift-cut machines for some ideas?