I'd guess this question comes from the negative feedback I gave on wirelessguy's deburr tool he's marketing. Even with that, I don't think the flash hole deburring operation is a big deal. I bet in 100 rounds, it might save you 3 of them moving a .1 around your group. Sometimes, yes, I suppose you might get a hole that's got a really big burr blocking it, depending on the brand, and lot number of the brass you're prepping. What I'm saying is I do think that if I am going to take the time to do it, I might as well do it the best I can, with the best available tool. When I decided flash hole uniforming might be worth the time spent, since you only have to do it once, I researched the most affordable, yet efficient methods of getting it done.
If I had a .17 I'd use
this one.
On larger cases I use
this one.
On my .204's I use
this one. See
video.
I wouldn't say you're doing it wrong, but I would say there's a possibility that by not using a tool that indexes off the case bottom, you may be defeating the purpose of doing the flash hole deburring operation. I think the goal is more to "uniform" them, not only deburr. As little as I think it helps groups, it's a precision sport, so we might as well try and go for uniformity where we can.
One area I'm having a problem with in my case prep, is in my RCBS prep center. Sure, it's quick and easy to chamfer the inside case mouth, deburr the outside case mouth. I also run the case down on a brass brush once as a last step to hopefully brush out any soot left in the neck, or leave them somewhat uniform. My problem with the whole thing is when chamfering and deburring using this machine, the case isn't held square in any chuck. It's up to me to try to hold the case perfectly upright so the tool makes a square cut. I don't know if something is bent inside mine or what, but all the tools wobble a little bit. I think the RCBS Trim Mate (prep center) leaves these operations wide open to operator error. You have to develop a feel for just how long to rest the case on the cutter. Too deep a chamfer, and too much deburr on the outside, will leave you with a razor edge on the case, which I doubt hurts anything, but it isn't very durable. The mouth probably melts a little, or gets blown away with the heat of ignition if it's too thin. Thinking "deburr" much more than "chamfer" is probably best with this machine, and a very light touch is required. It should also only be done on a case that's been trimmed square, and not once once fired cases that were already prepped once. I guess people have been doing these operations with the little handheld tools for years, even though it may not be the most precision way to do it. I think I read
this a few years ago. The part on chamfer/deburr particularly made sense.
Maybe I shouldn't even worry about the flash hole uniforming until I'm willing to advance to neck sizing. I guess I figure if it can help just a little, and doesn't add too many hours to prepping a batch of 1000 brass, why not do it? It can't hurt.
) and end up pulling up a dummy round out of my ammo box 
to know it's not what I want, and not what I'd recommend. Your machinist may have 25 years experience, but I used to be a CAD drafter, so I understand exactly how your tool works, and how it could easily be much better.
