Thanks to all for contributing your intonation experience with Ibanez SR basses with mono-rails!
Before I reply to individual posts, I would like to add that I bought a second Ibanez SR Bass, this time an 4-string SR5000. And you won't believe it - the bass has the same problem getting the intonation of the lowest string right.
This happens with my favorite strings, a set of Thomastik JF344 with 0.100" gauge of the E-string, which is quite a normal gauge for an E-string. With the intonation screw fully screwed out, which shifts the saddle all the way forwards to the pickups, the tone on the 12th fret is still flat.
Because there is still minimal space of about 1.5 mm at the end of the track, the saddle is sliding on, when the intonation screw is fully screwed out, I decided to buy and try a longer intonation screw, which is 35 mm long instead of 30 mm screw the bass came with. And with this longer screw with the saddles at the very end of the track, I was able to get just the right intonation adjustment for the E-string (see picture below).
What sense do mono-rails have installed that much backwards?? That it saddles have to be shifted as far forwards as possible to get correct intonation. Which limits the adjustment for different string gauges and action height enormously and even hinders the correct intonation adjustment for some setups and strings?