From experience I can say that the only way to keep them apart is to actively keep them apart. This is much harder than to lay two different tracks as its a process that requires you to use advanced detection rails and stuffs. I've tried minecarts between them, linked with railcraft and otherwise and they keep going silly.
As for the randomness equalizing after long enough distances,,, I could probably figure out the chances of the random chances for each section of track being equal but,,, Its statistically unlikely for them to be equal. This leads to one cart taking longer time than the other thus eventually they will collide.