Assessing repeatability requires some number of repeats.
Not necessarily a large number of units, but at least
multiple touchdowns, teardowns etc. to make sure you
have a good chance of getting the same answer next
wafer or next year. You depend on your cal lab for the
equipment for the most part, and worry about the stuff
that's on you - fixturing, cabling, ambient noise, self-
calibration, control units and like that.
Sure, everybody wants ppb confidence off one unit. Too
bad about that. Usually you have to work for it.
I would think that your organization, if this is an ongoing
business, has some standards for test development, what
level of accuracy / repeatability is expected and what
proof suffices.
Once you have demonstrated that the system is short-
term and across-teardown stable, if it goes off the rails
presumably it's the sustaining engineer's job to right it.
Just don't make the poor guy any more miserable.