OK Michal, you've got me thinking when you referred to the out of range controllers.
I've figured something out, that may not be very elegant but could work.
In my test scene I've created a large rectangle and measured this. On one linear array, I've followed your suggestion to animate the padding start, so over lets say 2000 frames this value is equal to the length of the spline. In the sequence operator, I've set the value of 'box' to occupy the distance of the spline, with a suitable padding value. As you know, the boxes travel along the spline, but as we're animating the 'start' of the array, there is no boxes behind it. And I want a continuous, looping array, no gaps in the train.
So I copied the RC array into a new one, set it to reverse, and inverted the keys for the padding values, so 0 is at the end, and the length of the spline value is now at the start. Beginning to look promising.
There are two issues doing this, the most obvious is in the first image, the reversed generator (in white) is offset and overlapping the non-reversed. I tried adjusting the keys in the curve editor, bumping it along to snuggle up behind, but this then means that the reversed one is out of synch, and pauses before a few frames before the final keyframe. I could live with a gap in the train, and I could clip the overlap or keep it all off camera, not ideal though.
Either way, I run into another problem and it's because I've added random rotation, which it will need. At the end of the loop, the boxes between loop 1 and the next, are out.
I may be able to work with this with some careful clipping, and some careful camera pointing and not rendering anything over the loop change, but it's not ideal, and if you are able to elaborate on this any further I'd appreciate it.
Ultimately I have to populate this with zillions of boxes on various splines. As with most of my models, Railclone has been used extensively to build this.