I also have two of the FS-1400/2, and two of the Holey rails. I also use the Betterley straight line connector, and haven't experienced any issues with alignment.
Now, having said that, if I had it to do over again, I would get the FS-3000 and two of the holey rails. The 3000 takes all of the effort/concern/caution/time (my own concerns or issues listed here) of connecting the two rails, ensuring that they are perfectly aligned, and not worrying about "if" they might have moved a tiny bit when repositioning the rails for another long cut on sheet goods. You can use one of the holey rails to cut across the sheet goods, you won't want to do that with the long rail.... As others have pointed out above, if you will be transporting the longer rail, just note the length and make sure you won't have issues hauling it around.
I eventually will probably get the FS-3000 and sale one or both of the FS-1400.