I never trusted turning off of a dummy or mandrel, and always try to use the centers as much as possible. Like you, I didn't have much luck doing them that way either. I have had luck chucking the butt section up and dialing it in with an indicator using It instead to chuck the shaft up. Then what I did was cut what I could with the router, but I matched 1/8-1/4 of the part closest to the joint using a manual tool. Usually the collar was phenolic, so That was easy to do, and the router cut the deco part better then a manual tool would, just didn't want to get too close to the butt joint with it, so I finished up with the manual tool.
Now I more less do what Jerry said. I'm starting to cut It closer to diameter before tapping My threads though, so I can do most of It using the center holes. I can tap Mine dead on these days with only a piloted tap, so If Your grinding Yours then you should have even better luck then I, as long as everything is dialed in before facing & grinding the threads. You should be able to get the diameter close before making Your threads. Nothing wrong with putting the ringwork on earlier while still using the centerholes as far as I know of. I'm starting to do that Myself. That will allow You to trim the rings some while decreasing the diameter of the shaft at the same time. Basically I'm already trimming that few inches of the shaft near the joint using a butt taper before I even drill & tap mine, and My ferrule has already made It to size. It's come to My attention that some tapers are really tight near the joint while trying to get the ferrule to size, But the taper I use allows for a larger joint even when the playing area is the diameter I want. Once I get that area to the diameter I want, then I drop to the butt taper to start blending the joint in.
Another thing I do, and this may be what Joey was talking about, but I champer the bore in the shaft large enough that even after the threads are In I can still run the shaft between centers with out a threaded mandrel should I choose to match the joint that way, or even more for maintaining purposes, and to help locate the pin in the threads.
Everyone has what works for them, But For me I prefer to trim as much as possible using center holes. I don't always do things the same everytime, but that's the one constant I usually do stick to.
Just a thought, but If By chance You already have a ferrule and tip installed while using the dummy, and triming, then that can throw things out too if the other end is being supported with a concave center on a tip. I've had that happen before, and because of It, I usually put My ferrules on last, unless I'm doing a open face ferrule, and can save the original center hole. A little bee's wax or tape will keep the glue out of the center hole from installing the ferrule, then You could run a trim pass on the ferrule at the same time. I just assume do it either way though, and installing the ferrule last is no big thing to me either, so on capped ferrules, instead of loosing my centerhole earlier on, I will just wait, and install them last right before the tip. New shafts are easy to center the ferrules on, and not loose any diameter from the shaft trying to blend things. It's used shafts that have the runnout and need to be shimmed sometimes to prevent that. I deal with enough of those in repair work to make the new shafts seem like a breeze.
The only threads I might would drive with are sanding mandrels, which I haven't used yet because I still hand blend most of mine, but even using those would just be for sanding, and I would probably do the trimming off centers the same or simular to what I do now.
I'm not saying that You can't drive the shaft with a mandrel and be successfull, because I'm sure some people do & have had good luck, just that I've had better luck using the center holes as much as I can.
Greg