As I don't own an R-D1s, I can't speak from experience.close-focus
There are only four adjustment screws in the R-D1 rangefinder mechanism, so, ignoring the vertical adjustment screw No. 3 already mentioned, the remaining screws adjust the sharpness of the finder patch (screw 1), infinity-focus horizontal adjustment (screw 2) and close-focus horizontal adjustment (screw 4).
Apart from giving better access to the screws under the hot shoe, removing the top plate allows access to screw 4. There is no other means of adjusting the rangefinder.
So, if screw 3 is inactive, there would be no way to adjust the vertical alignment, short of bending it or whacking it with a blunt instrument! Unless of course the R-D1s rangefinder mechanism was redesigned - which I think is very unlikely as the R-D1s is a rebadged R-D1 with a firmware upgrade. It would make no sense for several reasons for Epson to go to the expense of redesigning the mechanism, especially as it would need to be quite radical: all Bessa rangefinders, of which the Epson is a variant, are very similar, including how they are adjusted.
Perhaps Epson tried to address the vertical misalignment in the R-D1s, and factory-set and locked the vertical alignment; then did not bother with the correct adjustment screw 4, since the alignment should not need resetting in future. This seems far-fetched: it would be foolish of Epson to assume that re-adjustment would never be needed.
Applying Occam's razor, I suspect a few cameras are anomalous (e.g. lct's and jvr's), which could be a fault, or deliberate for whatever reason (e.g. a variation in manufacture) - this could equally affect the R-D1 (though there have been no reports in this forum) as well as the R-D1s.
Adding weight to this, is the post in this forum by an R-D1s owner who reported that a camera technician found screw 4 disconnected from the mechanism for no good reason, and once reconnected, the camera's vertical alignment could be set perfectly.
