Here are some things I found from filling and cutting many tone holes.
I have tried many different glues. My favorite to fill tone holes with grenadilla dust is actually thin super glue. I found it glues best to the tone hole (in comparison with thicker super glues). I've also tried various degrees of thicked thin super glue and this worked good too as long as it wasn't too thick already. You need to be careful but IME it's possible to get the thin super glue to where you want it. Like John, I also found it's crucial to start with glue, then add dust. Same as crack repair, putting the dust first will make the glue just soak into the dust and not really glue to whatever is under it much.
I've tried several types of slow and fast (5-minute) epoxy glues. I also thin the epoxy with heat when needed. All were fine in general, but I found some issues. 5-minute epoxies that I've tried (about four types I think) all dried in that time, but took so much longer to become really hard. Even then, they weren't as hard as slow epoxy or super glue for this purpose in a reasonable amount of time. It just seemed to take days to become reasonably hard. Slow epoxy is usually too low, though I use it sometimes for more serious fills (i.e. a big chunk is missing, usually with reinforcement stainless steel).
As far as filling, something that can help is making teflon coated "blockers". Sounds fancy, but this is just some more or less random parts with teflon sheet glued to them, to put where you don't want the glue to go to. You can put rods inside tone holes, tenons, etc. for this. Here is an example of using this method on a "jig" to make an epoxy extension to a key:
http://farm7.staticflickr.com/6208/6098983435_a1b89c0bab_z.jpg
For cutting tone holes I use a few tools. Some are hardened steel with teeth. Some I make myself, mostly from plastic or brass rods, with sandpaper glued to them. Sometimes I use something like a boring cutting tool on a mill to cut the tone hole. You can make sure the tone hole is centerd and level by putting a close fitting rod held by the mill inside the tone hole (for centering and leveling).
It's true that a flat surface of a tone hole can work, but the clarinet left hand ring finger is a tricky example. It's closed by a finger and doesn't need to be adjusted with any other key. I think for tone holes closed by fingers, the less sharp edge of "flat" tone holes is actually better and more comfortable. For tone holes closed by keys IMO the thinner and sharper (but not too sharp) edge has advantages. It would require less pressure from the pad to seal. The example I like is from the kids section in the local science museum. They have a chair full of nails you can sit on and a chair with only one nail...