In practice it's less a problem than it might seem.
1) You can check your own lens and use it accordingly. IMO you have to do this anyway, because besides the different factory optimizations, you'll find sample variations and lens/body mating variations. With a ruler test like the one above, mine turned out to be optimized for closest distance at f2.2. So I shoot at that aperture, or else at f5.6, with no problems.
2) As mentioned above: the smaller the aperture and the farther away, the less you can see focus shift anyway – it's compensated by DOF. But f 5.6 is as far as I like to stop down, because at smaller apertures the lens becomes quite contrasty, losing the 'classic' character that was the reason for buying it in the first place.
BTW, 50 pre-aspherical Summiluxes do exhibit some focus shift. Did you mean aspherical?