Odin, Personally, for the reasons you mentioned, I would not use those couplings. That is because: 1.) I over-engineer everything. 2.) The machines I generally am involved with require a high degree of accuracy. 3.) I'm as much a zealot as you are, maybe worse.
Having said all that, there are reasons for less extremes. Trading a bit of accuracy for a bit of "cushion", easy aligning, less cost etc.
Building an accurate mill requires you to design stiffness into and compliance out of the machine.
Instead of rubber/plastic membered couplings, you might consider metal bellows torsion resistant type coupling, direct mounting or a belt drive arrangement. All have pros & cons of their own.
Infinite budget? hollow spindle AC servo mounted directly on the ballscrew. If the application permits, round or flat linear motor(s).