I've just cut 6 sheets of ply for some cabinets. In the past I only had one 1400 rail and one 800 rail, and cutting up a full sheet was a pain. The ones I've just done I used 2x1400 rails joined with 2 of the joining bars.
My experience was that it is quite hard to get them 'spot on', but fairly straightforward to get them 'close enough' (and I am a bit of a perfectionist too!).
My first cuts after joining, I trimmed a few mm off the factory edge, then rotated the joined rails 180 degrees to cut the ply strip to the desired width. When I checked, the strip was just shy of 1mm wider in the centre than at the ends (therefore the rail assembly was bowed by less than 0.5mm).
Even with my longest (1800mm/6') level, I wasn't able to measure any deviation in the rail. I couldn't detect it by eye either, looking down the length (not surprising, really - 0.5mm over 2800mm is, as far as I'm concerned, negligible). It really didn't make much difference, but on the future rips instead of measuring/marking the required width just at the ends, I also did so in the centre, and lined up the rail at all three points. If the centre was out, just a slight nudge in the centre of the rail (with the ends clamped) was sufficient to move it slightly. Having said that, I would guess that based on the flexibility of aluminium, you could move the centre of a 3m rail by a few tenths of a mm in the same fashion (though I don't have a 3m rail to check that with).
Checking the rips after cutting, there was still some slight deviation in the widths, generally around 0.5mm. Realistically, that's as accurate as you can expect from timber, marked with a pencil. If you're trying to achieve better accuracy than that, then in my opinion you're going to fail, frustrating yourself in the process.
As a slight aside, I used to work in a kitchen factory where 3050mm long MFC sheets were cut up all day long on a very large & expensive panel saw; it was common to find that the finished pieces were sometimes +/-0.5mm from where they were supposed to be.
If you can afford it, and have room to store it securely, buy the 3m rail if it makes you feel better. If not, join the shorter rails, and take care whilst aligning & using them. It's not a big deal. Get over it (meant in the nicest possible way!).