I'm not really sure if anyone would do this but the tool that would be used to make something perfectly round would be a lathe.
I have heard of serious long range target shooters using a lathe to hand-make bullets for improved accuracy on the powder burner side. It seems like overkill for an air gun pellet though.
Someone who is more into the target shooting side can comment better than me but if the goal is maximum accuracy by removing as much of the variability between pellets as possible, my understanding is that this is most commonly achieved by: visually inspecting pellets and removing ones with damaged skirts, weighing them and sorting them into separate bags with matching weights and then possibly sizing them for your bore.
I haven't heard of anyone taking it a step further by then truing, sanding and polishing the skirts of each pellet in a lathe but that doesn't mean that nobody has ever done it. I might be tempted if I competed at the highest level.
My thought would be that, to have the desired effect, you would have to do it on a very high quality lathe. Those cheap $130 hobby lathes that you see on eBay are not know for being terribly precise in terms of making things perfectly round and even all the way around, so I don't know if they would be counter-productive for pellets.
Either way, it would be horribly tedious to use any tool to round off every pellet skirt. I'd be inclined to buy some high quality pellets like the Air Arms brand and then just remove any ones with damaged skirts with a visual inspection. I can't remember what they are called but people who use lathes use a special tool to measure how perfect,y round something is. Perhaps it might be better to use something like that to identify and remove the least round ones.