So I spent 1/2 hour inspecting the collet and I could not measure any real deviation from jaw to jaw that would account for the runout I measured.
I ran a few cases through it, measuring the runout on the outside of the neck before and after resizing, and they came out of the collet die exactly as straight as when they came out of the rifle chamber (around .001" T.I.R.).
The collet die forms the neck bore slightly tapered, less than .001" larger at the mouth than at the shoulder, but enough to be noticeable.
As a result, the gage pin that fits all the way through is free to move around at the case mouth (it wobbles slightly) which leads to erroneous runout measurements
The bushing die does not make the neck bore perfectly cylindrical either. Depending on how the gage pin is inserted, the necks can have apparent runout (when measured over the pin rather than the neck O.D.) after being run through it as well.
Nothing wrong with my 6 x 47 Lapua collet die.